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GlyGen data model and processing workflow

Robel Kahsay, Jeet Vora, Rahi Navelkar, Reza Mousavi, Brian Fochtman, Xavier Holmes, Nagarajan Pattabiraman, Rene Ranzinger, Rupali Mahadik, Tatiana Williamson, Sujeet Kulkarni, Gaurav Agarwal (+12 others)
2020 Bioinformatics  
This application note describes the GlyGen data model, processing workflow and the data access interfaces featuring programmatic use case example queries based on specific biological questions.  ...  The GlyGen project is a data integration, harmonization, and dissemination project for carbohydrate and glycoconjugate related data retrieved from multiple international data sources including UniProtKB  ...  In this processing and integration workflow, data are retrieved Fig. 1 . GlyGen data processing workflow showing various steps.  ... 
doi:10.1093/bioinformatics/btaa238 pmid:32324859 pmcid:PMC7320628 fatcat:2zcsp4mfs5bw7apagldi2lkm24

Bioinformatics tools developed to support BioCompute Objects

Janisha A Patel, Dennis A Dean, Charles Hadley King, Nan Xiao, Soner Koc, Ekaterina Minina, Anton Golikov, Phillip Brooks, Robel Kahsay, Rahi Navelkar, Manisha Ray, Dave Roberson (+3 others)
2021 Database: The Journal of Biological Databases and Curation  
BioCompute Objects (BCOs) provide the requisite support for communication of HTS data analysis that includes support for workflow, as well as data, curation, accessibility and reproducibility of communication  ...  and an increase in the types of data generated.  ...  Food and Drug Administration (75F40119C10136 and HHSF223201510129C to RM), U.S. National Institute of Health, Glycoscience Common Fund (1U01GM125267 to RM) and U.S.  ... 
doi:10.1093/database/baab008 pmid:33784373 fatcat:32edkjmnonbjnhmid5lcf3prre

Enhancing the interoperability of glycan data flow between ChEBI, PubChem, and GlyGen [article]

Rahi Navelkar, Gareth Owen, Venkatesh Mutherkrishnan, Paul Thiessen, Evan Bolton, Tiejun Cheng, Nathan Edwards, Michael Tiemeyer, Matthew Campbell, Maria Martin, Jeet Vora, Robel Kahsay (+1 others)
2021 bioRxiv   pre-print
This paper outlines a workflow developed in collaboration between GlyGen, ChEBI, and PubChem to improve the visibility and connectivity of glycan data across these resources.  ...  The current PubChem, ChEBI, and GlyTouCan mappings can be downloaded from GlyGen(  ...  GlyGen data processing and integration framework is utilized to quality control and standardized this data which is supplied to GlyGen portal . .  ... 
doi:10.1101/2021.06.17.448729 fatcat:7crcyk55yffvfieih24k55yj44

The human O-GlcNAcome database and meta-analysis

Eugenia Wulff-Fuentes, Rex R. Berendt, Logan Massman, Laura Danner, Florian Malard, Jeet Vora, Robel Kahsay, Stephanie Olivier-Van Stichelen
2021 Scientific Data  
Found in almost all living organisms, this post-translational modification of serine and threonine residues is highly conserved and key to biological processes.  ...  With half of the primary research articles using human models, the O-GlcNAcome recently reached a milestone of 5000 human proteins identified.  ...  We thank the GlyGen project and Michael Tiemeyer, Ph.D., for their interest and support in finalizing the O-GlcNAc database.  ... 
doi:10.1038/s41597-021-00810-4 pmid:33479245 pmcid:PMC7820439 fatcat:wnel6hh5cfgotlustorc2pp7wi

Differential expression of glycosyltransferases identified through comprehensive pan-cancer analysis [article]

Hayley M Dingerdissen, Jeet Vora, Edmund Cauley, Amanda Bell, Charles Hadley King, Raja Mazumder
2021 bioRxiv   pre-print
generation of data-driven cancer biomarker hypotheses.  ...  This work is expected to improve the understanding of glycosylation in cancer by transparently defining the space of glycosyltransferase enzymes and harmonizing variable experimental data to enable improved  ...  (former), and labmates Yu Hu, Yu Fan, Quan Wan, Ting-Chia Chang, and Brian Fochtman for significant algorithm, pipeline, and data contributions; current labmates, especially Xiying Ding, Naila Gulzar,  ... 
doi:10.1101/2021.06.15.448506 fatcat:wsbyqlmwm5fclcgqqz2gmxgayi

Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database

Florian Malard, Eugenia Wulff-Fuentes, Rex R Berendt, Guillaume Didier, Stephanie Olivier-Van Stichelen
2021 Database: The Journal of Biological Databases and Curation  
Post-translational modifications (PTMs) are ubiquitous and essential for protein function and signaling, motivating the need for sustainable benefit and open models of web databases.  ...  We particularly emphasized our workflow, involving a mostly automatized and self-maintained database, including machine learning approaches for text mining.  ...  Acknowledgements We thank GlyGen (  ... 
doi:10.1093/database/baab039 pmid:34279596 pmcid:PMC8288053 fatcat:s5p3bqsr7faj5gcy32exntb5rq

Towards a standardized bioinformatics infrastructure for N- and O-glycomics

Miguel A. Rojas-Macias, Julien Mariethoz, Peter Andersson, Chunsheng Jin, Vignesh Venkatakrishnan, Nobuyuki P. Aoki, Daisuke Shinmachi, Christopher Ashwood, Katarina Madunic, Tao Zhang, Rebecca L. Miller, Oliver Horlacher (+12 others)
2019 Nature Communications  
Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N- and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental  ...  This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR.  ...  The current model requires submission of MS raw data to GlycoPOST, whilst MIRAGE and GlycoWorkbench files are uploaded and read by the UniCarb-DR submission workflow.  ... 
doi:10.1038/s41467-019-11131-x pmid:31332201 pmcid:PMC6796180 fatcat:v76clag22jhi5gx6wnvx6yzaoe

Tools for generating and analyzing glycan microarray data

Akul Y Mehta, Jamie Heimburg-Molinaro, Richard D Cummings
2020 Beilstein Journal of Organic Chemistry  
We then highlight a number of tools for the analysis of glycan microarray data such as data repositories, data visualization and manual analysis tools, automated analysis tools and structural informatics  ...  In this review, we describe the intricacies of the generation of glycan microarray data and the experimental methods for studying binding.  ...  Acknowledgements The authors would like to thank Zachary Klamer, Johnathan Hall and Brian Haab (MotifFinder, SignalFinder) along with Lachlan Coff and Andrew Guy (CCARL), for help with their software.  ... 
doi:10.3762/bjoc.16.187 pmid:32983270 pmcid:PMC7492694 fatcat:svk7whxb3zbo3k5egj5jybyvge

14th Annual Biocuration Conference (virtual) - Abstracts from the invited speakers talks and poster session presentations [article]

Federica Quaglia
2021 Zenodo  
booklet of the 14th Annual Biocuration Conference (virtual), including invited speakers talks and poster session presentations  ...  We present the flag workflow, data from the process, and describe a method we use to search for new publication of terms placed on hold.  ...  The data that passes all QC checks is integrated in the GlyGen ( database and is publicly available.  ... 
doi:10.5281/zenodo.5570276 fatcat:nlbkkzkhfvhdddqu4ypzh247iy

Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens [article]

Santosh Renuse, Patrick M Vanderboom, Anthony D. Maus, Jennifer V. Kemp, Kari M. Gurtner, Anil K. Madugundu, Sandip Chavan, Jane A. Peterson, Benjamin J. Madden, Kiran K. Mangalaparthi, Dong-Gi Mun, Smrita Singh (+5 others)
2020 medRxiv   pre-print
An ensemble machine learning-based model for determining COVID-19 positive samples was created using fragment ion intensities in the PRM data.  ...  We then developed an automated antibody capture-based workflow coupled to targeted high-field asymmetric ion mobility spectrometry (FAIMS) - parallel reaction monitoring (PRM) assays on an Orbitrap Exploris  ...  Acknowledgments The following reagent was deposited by the Centers for Disease Control and Prevention and obtained through BEI Resources, NIAID, NIH: SARS-Related Coronavirus 2, Isolate USA-WA1/2020, Gamma-Irradiated  ... 
doi:10.1101/2020.08.05.20168948 fatcat:gd5evdkfm5dkxfcthoe3x7vdoe

Differential Quantitative Determination of Site-Specific Intact N-Glycopeptides in Serum Haptoglobin between Hepatocellular Carcinoma and Cirrhosis Using LC-EThcD-MS/MS

Jianhui Zhu, Zhengwei Chen, Jie Zhang, Mingrui An, Jing Wu, Qing Yu, St. John Skilton, Marshall Bern, K. Ilker Sen, Lingjun Li, David M. Lubman
2018 Journal of Proteome Research  
Herein, we developed a workflow that involved advanced methodologies, the EThcD-MS/MS fragmentation method and data interpretation software, for differential analysis of the microheterogeneity of site-specific  ...  Intact N-glycopeptide analysis remains challenging due to the complexity of glycopeptide structures, low abundance of glycopeptides in protein digests, and difficulties in data interpretation/quantitation  ...  ACKNOWLEDGMENTS We acknowledge the support of this work from the National Cancer Institution under grants 1R01 CA160254 (DML), U01 CA225753 (DML) and R50 CA221808 (JZ) and from the National Institutes  ... 
doi:10.1021/acs.jproteome.8b00654 pmid:30370771 pmcid:PMC6465142 fatcat:4aiiacqcubejhctxjqydl7ws7y

SILAC-Based Quantitative Proteomic Analysis of Diffuse Large B-Cell Lymphoma Patients

Ulla Rüetschi, Martin Stenson, Sverker Hasselblom, Herman Nilsson-Ehle, Ulrika Hansson, Henrik Fagman, Per-Ola Andersson
2015 International Journal of Proteomics  
We could identify over 3,500 proteins; more than 1,300 were quantified in all patients and 87 were significantly differentially expressed.  ...  two groups of DLBCL patients with totally different clinical outcome: (i) early relapsed or refractory and (ii) long-term progression-free patients.  ...  Acknowledgments Malin Ageberg, Department of Hematology and Transfusion Medicine, BioMedical Centre, Lund University, is greatly acknowledged for providing the DLBCL cell lines and for expert advice on  ... 
doi:10.1155/2015/841769 pmid:26060582 pmcid:PMC4427854 fatcat:bxfjou7t3bg27jk6piolvj3sou

Proteomic Changes in Chicken Plasma Induced by Salmonella typhimurium Lipopolysaccharides

Balamurugan Packialakshmi, Rohana Liyanage, Jackson O. Lay, Sarbjeet K. Makkar, Narayan C. Rath
2016 Proteomics Insights  
The objective was to identify plasma proteomic changes in an avian model of inflammation. Chickens were treated with either saline or LPS, and blood was collected at 24 hours postinjection.  ...  These differentially expressed proteins are associated with immunomodulation, cytokine changes, and defense mechanisms, which may be useful as candidate biomarkers of infection and inflammation.  ...  Acknowledgments The authors thank Scott Zornes, Sonia Tsai, and Wally McDonner for assistance.  ... 
doi:10.4137/pri.s31609 pmid:27053921 pmcid:PMC4818023 fatcat:zvzcbuujb5c65nfbo7bl6afcsa

COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model

Nikhita Gogate, Daniel Lyman, Amanda Bell, Edmund Cauley, Keith A Crandall, Ashia Joseph, Robel Kahsay, Darren A Natale, Lynn M Schriml, Sabyasach Sen, Raja Mazumder
2021 Briefings in Bioinformatics  
We have curated 145 COVID-19 biomarkers by developing a novel cross-cutting disease biomarker data model that allows integration and evaluation of biomarkers in patients with comorbidities.  ...  The heterogeneous data pose challenges for efficient extrapolation of information into clinical applications.  ...  curator); Nuerye Ainiwan (bioinformatics curator); Pranav Mishra (bioinformatics curator); Renee Long (bioinformatics curator); Rishab Desai (bioinformatics curator); Rita Mazumder (Asst. coordinator and  ... 
doi:10.1093/bib/bbab191 pmid:34015823 pmcid:PMC8195003 fatcat:bv7cbd7unfcldhtykjofmmqe3q

Rapid and Accurate Differentiation of Mycobacteroides abscessus Complex Species by Liquid Chromatography-Ultra-High-Resolution Orbitrap™ Mass Spectrometry

Amol O. Bajaj, E. Susan Slechta, Adam P. Barker
2022 Frontiers in Cellular and Infection Microbiology  
Data analysis showed ~7-17 proteoforms potentially able to differentiate between subspecies.  ...  This assay identified 150, 130, 140 and 110 proteoforms with isocratic elution and 230, 180, 200 and 190 proteoforms with gradient elution for M. abscessus (ATCC 19977), M. massiliense (DSM 45103), M.  ...  Joanna Freeke and Dr. J. Benjamin Stielow all employees of Thermo Fisher Scientific for providing all the help with proteomic data analysis using the proprietary software.  ... 
doi:10.3389/fcimb.2022.809348 pmid:35356534 pmcid:PMC8959847 fatcat:bh3k3cngvreuxerdzudgwbmaxa
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