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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
Despite accumulating evidence supporting a role for glycosylation in cancer progression and prognosis, the complexity of the human glycome and glycoproteome poses many challenges to understanding glycosylation-related events in cancer. In this study, a multifaceted genomics approach was applied to analyze the impact of differential expression of glycosyltransferases (GTs) in 16 cancers. An enzyme list was compiled and curated from numerous resources to create a consensus set of GTs. Resulting
more » ... zymes were analyzed for differential expression in cancer, and findings were integrated with experimental evidence from other analyses, including: similarity of healthy expression patterns across orthologous genes, miRNA expression, automatically-mined literature, curation of known cancer biomarkers, N-glycosylation impact, and survival analysis. The resulting list of GTs comprises 222 human enzymes based on annotations from five databases, 84 of which were differentially expressed in more than five cancers, and 14 of which were observed with the same direction of expression change across all implicated cancers. 25 high-value GT candidates were identified by cross-referencing multimodal analysis results, including PYGM, FUT6 and additional fucosyltransferases, several UDP-glucuronosyltransferases, and others, and are suggested for prioritization in future cancer biomarker studies. Relevant findings are available through OncoMX at, and the overarching pipeline can be used as a framework for similarly analysis across diverse evidence types in cancer. 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 generation of data-driven cancer biomarker hypotheses.
doi:10.1101/2021.06.15.448506 fatcat:wsbyqlmwm5fclcgqqz2gmxgayi


Hridesh Shah, ijar, Dhruv Shah, Jeet Shah, Akshat Shah, Karan Shah, Krupal Vora, ijar, ijar, ijar, ijar, ijar
2018 International Journal of Advanced Research  
Int. J. Adv. Res. 6(11), 974-979 977 successful testing and deployment our system requires user feedback for updates and modifications in our algorithm. Maintenance: As our system needs constant updates regarding soil quality and efficiency of our system, the maintenance of our system is very crucial. The user feedback enables us to know if our system is working as per user expectation. Changes help us modify our analysis algorithm for improving our analysis on suitable crop lists.
doi:10.21474/ijar01/8083 fatcat:k3ihf364xzgm5ofkj5grmn3rqm

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  
AbstractOver the past 35 years, ~1700 articles have characterized protein O-GlcNAcylation. 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. Herein, we provide an extensive inventory of human O-GlcNAcylated proteins, their O-GlcNAc sites,
more » ... ication methods, and corresponding references ( In the absence of a comprehensive online resource for O-GlcNAcylated proteins, this list serves as the only database of O-GlcNAcylated proteins. Based on the thorough analysis of the amino acid sequence surrounding 7002 O-GlcNAc sites, we progress toward a more robust semi-consensus sequence for O-GlcNAcylation. Moreover, we offer a comprehensive meta-analysis of human O-GlcNAcylated proteins for protein domains, cellular and tissue distribution, and pathways in health and diseases, reinforcing that O-GlcNAcylation is a master regulator of cell signaling, equal to the widely studied phosphorylation.
doi:10.1038/s41597-021-00810-4 pmid:33479245 pmcid:PMC7820439 fatcat:wnel6hh5cfgotlustorc2pp7wi

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
GlyGen data processing and integration framework is utilized to quality control and standardized this data which is supplied to GlyGen portal (Kahsay, Vora et al. 2020) .  ... 
doi:10.1101/2021.06.17.448729 fatcat:7crcyk55yffvfieih24k55yj44

Bringing Generalization to Deep Multi-View Pedestrian Detection [article]

Jeet Vora, Swetanjal Dutta, Kanishk Jain, Shyamgopal Karthik, Vineet Gandhi
2022 arXiv   pre-print
Multi-view Detection (MVD) is highly effective for occlusion reasoning in a crowded environment. While recent works using deep learning have made significant advances in the field, they have overlooked the generalization aspect, which makes them impractical for real-world deployment. The key novelty of our work is to formalize three critical forms of generalization and propose experiments to evaluate them: generalization with i) a varying number of cameras, ii) varying camera positions, and
more » ... lly, iii) to new scenes. We find that existing state-of-the-art models show poor generalization by overfitting to a single scene and camera configuration. To address the concerns: (a) we propose a novel Generalized MVD (GMVD) dataset, assimilating diverse scenes with changing daytime, camera configurations, varying number of cameras, and (b) we discuss the properties essential to bring generalization to MVD and propose a barebones model to incorporate them. We perform a comprehensive set of experiments on the WildTrack, MultiViewX, and the GMVD datasets to motivate the necessity to evaluate the generalization abilities of MVD methods and to demonstrate the efficacy of the proposed approach. The code and the proposed dataset can be found at
arXiv:2109.12227v4 fatcat:26umtpyx2nfe5jb6hzecy3jhfm

Comparing results of Endoscopic microdiscectomy and conventional discectomy for lumbar disc disease: A short term study

Dr. Padmanabh Vora, Dr. Parth Thaker, Dr. Jeet Gandhi, Dr. Yash Gupta, Dr. Himanshu Panchal, Dr. Mukund Prabhakar
2019 International Journal of Orthopaedics Sciences  
Chronic lumbo-sacral pain is a common and challenging clinical entity in pain management centre. The most commonly involved surgical indication are intractable leg or back pain and significant functional impairment that have been unresponsive to conservative measures. This is a level 2 evidence study where we have studied results of endoscopic discectomy and compared it to conventional discectomy procedure. Material and Methods: We selected 40 patients with severe low back pain radiating to one
more » ... or both lower limbs, which has failed to resolve after prolonged conservative treatment and have less than level 3 disc prolapse. Oswestry Disability Index (For Low Back Pain) was recorded with questionnaire response and used as clinical tool for assessment. Results: Mean age of 40 patients was found to be 42.9 year with 80% patients having paracentral disc protrusion. Average operative time for endoscopic discectomy was 103 minutes which was higher than conventional discectomy (78 minutes). However, there was minimal blood loss compared to conventional discectomy. Based on ODI score, both endoscopic and conventional discectomy offered similar results in all grades. Conclusion: Endoscopic discectomy is a novel, safe and effective method that minimizes invasiveness of the surgical approach. Results achieved with this method are comparable to those achieved with open discectomy in terms of relief of symptoms on longer follow up, and is significantly better in terms of early mobilisation and morbidity as there is minimal tissue trauma.
doi:10.22271/ortho.2019.v5.i1a.06 fatcat:bj3hic5a7bft5hxinjcxtczjd4

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  
Summary Glycoinformatics plays a major role in glycobiology research, and the development of a comprehensive glycoinformatics knowledgebase is critical. 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
more » ... le international data sources including UniProtKB, GlyTouCan, UniCarbKB and other key resources. Availability and Implementation GlyGen web portal is freely available to access at The data portal, web services, SPARQL endpoint, and GitHub repository are also freely available at,,, and, respectively. All code is released under license GNU General Public License version 3 (GNU GPLv3) and is available on GitHub The datasets are made available under Creative Commons Attribution 4.0 International (CC BY 4.0) license Supplementary information Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btaa238 pmid:32324859 pmcid:PMC7320628 fatcat:2zcsp4mfs5bw7apagldi2lkm24

Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results [article]

Gil Alterovitz, Dennis A Dean, Carole Goble, Michael R Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Charles Hadley S King, Dan Taylor, KanakaDurga Addepalli, Elaine Johanson (+23 others)
2017 bioRxiv   pre-print
Precision medicine can be empowered by a personalized approach to patient care based on the patient's or pathogen's unique genomic sequence. For precision medicine, genomic findings must be robust and reproducible, and experimental data capture should adhere to FAIR guiding principles. Moreover, precision medicine requires standardized reporting that extends beyond wet lab procedures to computational methods. Rapidly developing standardization technologies can improve communication and
more » ... of genomic sequence data analysis steps by utilizing concepts defined in the BioCompute framework, such as error domain, usability domain, verification kit, and provenance domain. These advancements allow data provenance to be standardized and promote interoperability. Thus, a resulting bioinformatics computation instance that includes these advancements can be easily communicated, repeated and compared by scientists, regulators, test developers and clinicians. Easing the burden of doing the aforementioned tasks greatly extends the range of practical application. Advancing clinical trials, precision medicine, and regulatory submissions requires an umbrella of standards that not only fuses these elements, but also ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCOs) offer that umbrella. Through standardized bundling of high-throughput sequencing studies under BCOs, regulatory agencies (e.g., FDA), test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, with the potential for decreasing the time and cost associated with next generation sequencing workflow exchange, reporting, and regulatory reviews.
doi:10.1101/191783 fatcat:6idjm4omhzasfofouk22akgdqy

Enabling precision medicine via standard communication of HTS provenance, analysis, and results

Gil Alterovitz, Dennis Dean, Carole Goble, Michael R. Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H. King, Dan Taylor, Elaine Johanson (+25 others)
2018 PLoS Biology  
A personalized approach based on a patient's or pathogen's unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (
more » ... es standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed, and compared by scientists, regulators, test developers, and clinicians. Easing the burden of performing the aforementioned tasks greatly extends the range of practical application. Large clinical trials, precision medicine, and regulatory submissions require a set of agreed upon standards that ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCOs) offer that standard and are freely accessible as a GitHub organization ( following the " principles for collaborative open standards development." With high-throughput sequencing (HTS) studies communicated using a BCO, regulatory agencies (e.g., Food and Drug Administration [FDA]), diagnostic test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, potentially decreasing the time and cost associated with next-generation sequencing workflow exchange, reporting, and regulatory reviews.
doi:10.1371/journal.pbio.3000099 pmid:30596645 pmcid:PMC6338479 fatcat:dh5fphvtazd5xlzu3vtl6cata4

Page 230 of National Union Catalog Vol. 32, Issue [page]

1958 National Union Catalog  
Singh, Sir Jeet, Raja, ed. and tr. BL2020.S5N28 1943 304.553 61-56156 Nanak, /st guru of the Sikhs, 1469-1538. The Jap Ji; the message of Guru Nanak.  ...  Vora, 1958. 164 p. 18 cm. 1. Roman law —Compends. 60-20648 MH-L Nanavati, ir Manilal Balabhai, 1877- The Indian rural problem, by Manilal B. Nanavati and J.J. Anjaria. 5th ed., largely rewritten.  ... 

Page 381 of National Union Catalog Vol. 38, Issue [page]

National Union Catalog  
Blue roses; or, Helen Malinofska’s marriage, by the author of ‘Vora, ‘Hotel du petit St. Jean,’ ‘Iseulte,’ ete London, Hi. 8.  ...  Address is sicned) 1 Dempster 1 Fisheries thind 1 Tithe Am 1c —— em astbt Dempster, Henry The decked welled fishing beat, and fisheries and fish tharket reform: being dialogues on these important sub jeets  ... 

OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data

Hayley M. Dingerdissen, Frederic Bastian, K. Vijay-Shanker, Marc Robinson-Rechavi, Amanda Bell, Nikhita Gogate, Samir Gupta, Evan Holmes, Robel Kahsay, Jonathon Keeney, Heather Kincaid, Charles Hadley King (+3 others)
2020 JCO Clinical Cancer Informatics  
Kiran Vora and Rahi Navelkar for thoughtful discussion regarding data set maintenance and related considerations.  ...  Sneh Talwar for assistance preparing draft figures and data tables; Peng Su for contributions to and support for mutation literature mining; Edmund Cauley and Daniel Lyman for manuscript review; and Jeet  ... 
doi:10.1200/cci.19.00117 pmid:32142370 pmcid:PMC7101249 fatcat:qijqv25waffovfheo77vm7meey

Conflict of Interest Disclosures

2019 Global Spine Journal  
Tunay Santaguida, Carlo Santivanez, Raul Santorcuato, Macarena Santos, Hugo Sapare, Sarang Saran, Neil Sarro, Angela Sasaki, Kandi Satanovsky, Alexandra Saville, Philip Savin, Dmitriy Savle, Jeet  ...  Perez, Julio Villarreal Barrera, Orlando Villas, Carlos Vinayek, Sheetal Viola, Á rpád Virk, Michael S Vissarionov, Sergey Visser, Thomas Vladimir, Klimov Volkov, Ivan von Glinski, Alexander Vora  ... 
doi:10.1177/2192568219852642 pmid:31211026 pmcid:PMC6555103 fatcat:g7ro6e55tbcwhpstzf4dw6bvzm

Page 3 of Herald of Freedom Vol. 5, Issue 43 [page]

1839 Herald of Freedom  
No lace fone Jeet in controversy, he Is Justly the prt P ; under a long protracted War, an 1: jwilleome in rolls neatly put up, Wrapped wil, : 7 NS y sti if . t . _ sepr ‘ . . ‘ | - bs - 3 4 - i ‘ “Tet  ...  Harrison, fy i } kU to aa oa : : = - ete ~ South of the State House, Ma i lik ’ ; ‘ ; & the most vorae | FeGressed | mark upon it hereafter, cits undeniable anc erences z 3 ‘ticul | IXER'S Patent Spring  ... 

Observations on the Solar Spots. By Alexander Wilson, M. D. Professor of Practical Astronomy in the University of Glasgow. Communicated by the Rev. Nevil Maskelyne, Astronomer Royal

Alexander Wilson, Nevil Maskelyne
1774 Philosophical Transactions  
Tlle following quotatior firnilll us with a remarkal)le inRance of this, alld will ferve to givs us a -view of ie ideas7 which he £-ame £<3 ettertaitl uporl thefe fub jeEts-. quod, ad indar mari-s nofiri  ...  expiratur whell fpeakiIzg of the fun's body: ssAtque ss ita hic liquorSigzeus (ut fic loqui liceat) eSt quafis ss vaAiW;mum luminum pelagus et male ignoum 4* quod fuss habet abyXas; occultos meatess vora  ... 
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