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https://www.readbyqxmd.com/read/29323256/splicing-of-platelet-resident-pre-mrnas-upon-activation-by-physiological-stimuli-results-in-functionally-relevant-proteome-modifications
#1
Giovanni Nassa, Giorgio Giurato, Giovanni Cimmino, Francesca Rizzo, Maria Ravo, Annamaria Salvati, Tuula A Nyman, Yafeng Zhu, Mattias Vesterlund, Janne Lehtiö, Paolo Golino, Alessandro Weisz, Roberta Tarallo
Platelet activation triggers thrombus formation in physiological and pathological conditions, such as acute coronary syndromes. Current therapies still fail to prevent thrombotic events in numerous patients, indicating that the mechanisms modulating platelet response during activation need to be clarified. The evidence that platelets are capable of de novo protein synthesis in response to stimuli raised the issue of how megakaryocyte-derived mRNAs are regulated in these anucleate cell fragments. Proteogenomics was applied here to investigate this phenomeon in platelets activated in vitro with Collagen or Thrombin Receptor Activating Peptide...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29314742/the-role-of-mass-spectrometry-and-proteogenomics-in-the-advancement-of-hla-epitope-prediction
#2
REVIEW
Amanda L Creech, Ying S Ting, Scott P Goulding, John Fk Sauld, Dominik Barthelme, Michael S Rooney, Terri A Addona, Jennifer G Abelin
A challenge in developing personalized cancer immunotherapies is the prediction of putative cancer-specific antigens. Currently, predictive algorithms are used to infer binding of peptides to human leukocyte antigen (HLA) heterodimers to aid in the selection of putative epitope targets. One drawback of current epitope prediction algorithms is that they are trained on datasets containing biochemical HLA-peptide binding data that may not completely capture the rules associated with endogenous processing and presentation...
January 3, 2018: Proteomics
https://www.readbyqxmd.com/read/29299837/brute-force-approach-for-mass-spectrometry-based-variant-peptide-identification-in-proteogenomics-without-personalized-genomic-data
#3
Mark V Ivanov, Anna A Lobas, Lev I Levitsky, Sergei A Moshkovskii, Mikhail V Gorshkov
In a proteogenomic approach based on tandem mass spectrometry analysis of proteolytic peptide mixtures, customized exome or RNA-seq databases are employed for identifying protein sequence variants. However, the problem of variant peptide identification without personalized genomic data is important for a variety of applications. Following the recent proposal by Chick et al. (Nat. Biotechnol. 33, 743-749, 2015) on the feasibility of such variant peptide search, we evaluated two available approaches based on the previously suggested "open" search and the "brute-force" strategy...
January 3, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29278999/detection-of-gelatin-adulteration-using-bio-informatics-proteomics-and-high-resolution-mass-spectrometry
#4
Charles T Yang, Dipankar Ghosh, Francis Beaudry
Following the internationalization of food production and manufacturing, a significant increase of food fraud was discovered, ranging from false label claims to the use of additives and fillers to increase profitability. The accidental or fraudulent mixing of animal products or by-products from different species is an important preoccupation for consumers with health or ethical concerns. Gelatin is widely used during food processing as well as in cosmetics, nutraceutics and medical formulations. It contains mainly type I, II and III collagen polypeptides...
December 26, 2017: Food Additives & Contaminants. Part A, Chemistry, Analysis, Control, Exposure & Risk Assessment
https://www.readbyqxmd.com/read/29258473/proteomics-analysis-and-proteogenomic-characterization-of-different-physiopathological-human-lenses
#5
Xiaohang Wu, Zhenzhen Liu, Xiayin Zhang, Dongni Wang, Erping Long, Jinghui Wang, Wangting Li, Weiyi Lai, Qianzhong Cao, Kunhua Hu, Weirong Chen, Haotian Lin, Yizhi Liu
BACKGROUND: The aim of the present study was to identify the proteomic differences among human lenses in different physiopathological states and to screen for susceptibility genes/proteins via proteogenomic characterization. METHODS: The total proteomes identified across the regenerative lens with secondary cataract (RLSC), congenital cataract (CC) and age-related cataract (ARC) groups were compared to those of normal lenses using isobaric tagging for relative and absolute protein quantification (iTRAQ)...
December 19, 2017: BMC Ophthalmology
https://www.readbyqxmd.com/read/29228611/proteogenomic-characterization-and-integrative-analysis-of-glioblastoma-multiforme
#6
Ying-Chun Song, Gai-Xia Lu, Hong-Wei Zhang, Xiao-Ming Zhong, Xian-Ling Cong, Shao-Bo Xue, Rui Kong, Dan Li, Zheng-Yan Chang, Xiao-Feng Wang, Yun-Jie Zhang, Ran Sun, Li Chai, Ru-Ting Xie, Ming-Xiang Cai, Ming Sun, Wei-Qing Mao, Hui-Qiong Yang, Yun-Chao Shao, Su-Yun Fan, Ting-Miao Wu, Qing Xia, Zhong-Wei Lv, David A Fu, Yu-Shui Ma
Glioblastoma multiforme (GBM), the most aggressive and lethal primary brain tumor, is characterized by very low life expectancy. Understanding the genomic and proteogenomic characteristics of GBM is essential for devising better therapeutic approaches.Here, we performed proteomic profiling of 8 GBM and paired normal brain tissues. In parallel, comprehensive integrative genomic analysis of GBM was performed in silico using mRNA microarray and sequencing data. Two whole transcript expression profiling cohorts were used - a set of 3 normal brain tissues and 22 glioma tissue samples and a cohort of 5 normal brain tissues and 49 glioma tissue samples...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29223802/proteogenomic-insights-into-uranium-tolerance-of-a-chernobyl-s-microbacterium-bacterial-isolate
#7
Gallois Nicolas, Alpha-Bazin Béatrice, Ortet Philippe, Barakat Mohamed, Piette Laurie, Long Justine, Berthomieu Catherine, Armengaud Jean, Chapon Virginie
Microbacterium oleivorans A9 is a uranium-tolerant actinobacteria isolated from the trench T22 located near the Chernobyl nuclear power plant. This site is contaminated with different radionuclides including uranium. To observe the molecular changes at the proteome level occurring in this strain upon uranyl exposure and understand molecular mechanisms explaining its uranium tolerance, we established its draft genome and used this raw information to perform an in-depth proteogenomics study. High-throughput proteomics were performed on cells exposed or not to 10μM uranyl nitrate sampled at three previously identified phases of uranyl tolerance...
December 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29221171/proteogenomic-analysis-prioritises-functional-single-nucleotide-variants-in-cancer-samples
#8
Shiyong Ma, Ranjeeta Menon, Rebecca C Poulos, Jason W H Wong
Massively parallel DNA sequencing enables the detection of thousands of germline and somatic single nucleotide variants (SNVs) in cancer samples. The functional analysis of these mutations is often carried out through in silico predictions, with further downstream experimental validation rarely performed. Here, we examine the potential of using mass spectrometry-based proteomics data to further annotate the function of SNVs in cancer samples. RNA-seq and whole genome sequencing (WGS) data from Jurkat cells were used to construct a custom database of single amino acid variant (SAAV) containing peptides and identified over 1,000 such peptides in two Jurkat proteomics datasets...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29218898/building-trans-omics-evidence-using-imaging-and-omics-to-characterize-cancer-profiles
#9
Arunima Srivastava, Chaitanya Kulkarni, Parag Mallick, Kun Huang, Raghu Machiraju
Utilization of single modality data to build predictive models in cancer results in a rather narrow view of most patient profiles. Some clinical facet s relate strongly to histology image features, e.g. tumor stages, whereas others are associated with genomic and proteomic variations (e.g. cancer subtypes and disease aggression biomarkers). We hypothesize that there are coherent "trans-omics" features that characterize varied clinical cohorts across multiple sources of data leading to more descriptive and robust disease characterization...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29213059/a-comprehensive-assessment-of-the-genetic-determinants-in-salmonella-typhimurium-for-resistance-to-hydrogen-peroxide-using-proteogenomics
#10
Sardar Karash, Rohana Liyanage, Abdullah Qassab, Jackson O Lay, Young Min Kwon
Salmonella is an intracellular pathogen infecting a wide range of hosts and can survive in macrophages. An essential mechanism used by macrophages to eradicate Salmonella is production of reactive oxygen species. Here, we used proteogenomics to determine the candidate genes and proteins that have a role in resistance of S. Typhimurium to H2O2. For Tn-seq, a saturated Tn5 insertion library was grown in vitro under either 2.5 (H2O2L) or 3.5 mM H2O2 (H2O2H). We identified two sets of overlapping genes required for resistance of S...
December 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29141959/an-integrative-strategy-to-identify-the-entire-protein-coding-potential-of-prokaryotic-genomes-by-proteogenomics
#11
Ulrich Omasits, Adithi R Varadarajan, Michael Schmid, Sandra Goetze, Damianos Melidis, Marc Bourqui, Olga Nikolayeva, Maxime Québatte, Andrea Patrignani, Christoph Dehio, Juerg E Frey, Mark D Robinson, Bernd Wollscheid, Christian H Ahrens
Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations. Our strategy toward accurate and complete genome annotation consolidates CDSs from multiple reference annotation resources, ab initio gene prediction algorithms and in silico ORFs (a modified six-frame translation considering alternative start codons) in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential of a prokaryotic genome...
December 2017: Genome Research
https://www.readbyqxmd.com/read/29132314/proteomics-in-non-human-primates-utilizing-rna-seq-data-to-improve-protein-identification-by-mass-spectrometry-in-vervet-monkeys
#12
J Michael Proffitt, Jeremy Glenn, Anthony J Cesnik, Avinash Jadhav, Michael R Shortreed, Lloyd M Smith, Kylie Kavanagh, Laura A Cox, Michael Olivier
BACKGROUND: Shotgun proteomics utilizes a database search strategy to compare detected mass spectra to a library of theoretical spectra derived from reference genome information. As such, the robustness of proteomics results is contingent upon the completeness and accuracy of the gene annotation in the reference genome. For animal models of disease where genomic annotation is incomplete, such as non-human primates, proteogenomic methods can improve the detection of proteins by incorporating transcriptional data from RNA-Seq to improve proteomics search databases used for peptide spectral matching...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29130603/proteogenomic-re-annotation-of-coccidioides-posadasii-strain-silveira
#13
Natalie M Mitchell, Andrew L Sherrard, Surendra Dasari, D Mitchell Magee, Thomas E Grys, Douglas F Lake
The aims of this study were to provide protein-based evidence upon which to re-annotate of the genome of C. posadasii, one of two closely related species of Coccidioides, a dimorphic fungal pathogen that causes coccidioidomycosis, also called Valley Fever. Proteins present in lysates and filtrates of in vitro grown mycelia and parasitic phase spherules from C. posadasii strain Silveira were analyzed using a GeLC-MS/MS method. Acquired spectra were processed with a proteogenomics workflow comprising a Silveira proteome database, a 6-frame translation of the Silveira genome and an ab initio gene prediction tool prior to validation against published ESTs...
November 12, 2017: Proteomics
https://www.readbyqxmd.com/read/29092937/an-accessible-proteogenomics-informatics-resource-for-cancer-researchers
#14
Matthew C Chambers, Pratik D Jagtap, James E Johnson, Thomas McGowan, Praveen Kumar, Getiria Onsongo, Candace R Guerrero, Harald Barsnes, Marc Vaudel, Lennart Martens, Björn Grüning, Ira R Cooke, Mohammad Heydarian, Karen L Reddy, Timothy J Griffin
Proteogenomics has emerged as a valuable approach in cancer research, which integrates genomic and transcriptomic data with mass spectrometry-based proteomics data to directly identify expressed, variant protein sequences that may have functional roles in cancer. This approach is computationally intensive, requiring integration of disparate software tools into sophisticated workflows, challenging its adoption by nonexpert, bench scientists. To address this need, we have developed an extensible, Galaxy-based resource aimed at providing more researchers access to, and training in, proteogenomic informatics...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29077059/network-driven-proteogenomics-unveils-an-aging-related-imbalance-in-the-olfactory-i%C3%AE%C2%BAb%C3%AE-nf%C3%AE%C2%BAb-p65-complex-functionality-in-tg2576-alzheimer-s-disease-mouse-model
#15
Maialen Palomino-Alonso, Mercedes Lachén-Montes, Andrea González-Morales, Karina Ausín, Alberto Pérez-Mediavilla, Joaquín Fernández-Irigoyen, Enrique Santamaría
Olfaction is often deregulated in Alzheimer's disease (AD) patients, and is also impaired in transgenic Tg2576 AD mice, which overexpress the Swedish mutated form of human amyloid precursor protein (APP). However, little is known about the molecular mechanisms that accompany the neurodegeneration of olfactory structures in aged Tg2576 mice. For that, we have applied proteome- and transcriptome-wide approaches to probe molecular disturbances in the olfactory bulb (OB) dissected from aged Tg2576 mice (18 months of age) as compared to those of age matched wild-type (WT) littermates...
October 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29068423/comprehensive-analysis-of-cancer-proteogenome-to-identify-biomarkers-for-the-early-diagnosis-and-prognosis-of-cancer
#16
REVIEW
Hem D Shukla
During the past century, our understanding of cancer diagnosis and treatment has been based on a monogenic approach, and as a consequence our knowledge of the clinical genetic underpinnings of cancer is incomplete. Since the completion of the human genome in 2003, it has steered us into therapeutic target discovery, enabling us to mine the genome using cutting edge proteogenomics tools. A number of novel and promising cancer targets have emerged from the genome project for diagnostics, therapeutics, and prognostic markers, which are being used to monitor response to cancer treatment...
October 25, 2017: Proteomes
https://www.readbyqxmd.com/read/29062388/highlights-from-the-win-2017-symposium-26-27-june-2017-paris-france-expediting-global-innovation-in-precision-cancer-medicine
#17
Will Davies
The Worldwide Innovative Networking (WIN) symposium brings together representatives from academic institutions, pharmaceutical partners, technology companies and charitable organisations from across the globe for an annual summit, discussing ongoing research and the latest developments in precision medicine. Now, in its seventh year, the aims of the WIN consortium's annual meeting, to foster communication and collaboration between members and deliver clinical trial results that improve the care and outcomes of patients are presented in open dialogue to encourage debate and discussion...
2017: Ecancermedicalscience
https://www.readbyqxmd.com/read/29059504/intersection-of-proteomics-and-genomics-to-solve-the-unsolved-in-rare-disorders-such-as-neurodegenerative-and-neuromuscular-diseases
#18
Andreas Roos, Rachel Thompson, Rita Horvath, Hanns Lochmüller, Albert Sickmann
Despite recent rapid advances in sequencing technologies, a significant proportion of patients with rare genetic disorders do not receive a genetic diagnosis after exhaustive testing, and even fewer have a potential therapeutic target identified. Taking rare neuromuscular and neurodegenerative disorders as a paradigm that can be extended to other rare Mendelian disorders, this viewpoint explores the opportunities that are brought about by the integration of genomics and proteomics, as well as the limitations and remaining challenges of this newly emerging field of proteogenomics...
October 23, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29046389/the-antibody-repertoire-of-colorectal-cancer
#19
Seong Won Cha, Stefano Bonissone, Seungjin Na, Pavel A Pevzner, Vineet Bafna
Immunotherapy is becoming increasingly important in the fight against cancers, utilizing and manipulating the body's immune response to treat tumors. Understanding the immune repertoire - the collection of immunological proteins - of treated and untreated cells is possible at the genomic, but technically difficult at the protein level. Standard protein databases do not include the highly divergent sequences of somatic rearranged immunoglobulin genes, and may lead to missed identifications in a mass spectrometry search...
October 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29039718/current-status-of-proteomics-of-soft-tissue-sarcomas
#20
Tadashi Kondo
Proteomics has been used in soft tissue sarcoma (STS) research in the attempts to improve the understanding of the disease background and develop novel clinical applications. Using various proteomics modalities, aberrant regulations of numerous intriguing proteins were identified in STSs, and the possible utilities of identified proteins as biomarkers or therapeutic targets have been explored. STS is an exceptionally diverse group of malignant diseases with highly complex molecular backgrounds and, therefore, an overview of the achievements and prospects of STS proteomics could enhance our knowledge of the possibilities and limitations of cancer proteomics...
October 25, 2017: Expert Review of Proteomics
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