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PathCards: multi-source consolidation of human biological pathways

Frida Belinky, Noam Nativ, Gil Stelzer, Shahar Zimmerman, Tsippi Iny Stein, Marilyn Safran, Doron Lancet
2015 Database: The Journal of Biological Databases and Curation  
The study of biological pathways is key to a large number of systems analyses.  ...  To address this, we exercised a combination of hierarchical clustering and nearest neighbor graph representation, with judiciously selected cutoff values, thereby consolidating 3215 human pathways from  ...  Conflict of interest. None declared.  ... 
doi:10.1093/database/bav006 pmid:25725062 pmcid:PMC4343183 fatcat:mf37aem2avhe7nhcqrcdgk32se

Rational confederation of genes and diseases: NGS interpretation via GeneCards, MalaCards and VarElect

Noa Rappaport, Simon Fishilevich, Ron Nudel, Michal Twik, Frida Belinky, Inbar Plaschkes, Tsippi Iny Stein, Dana Cohen, Danit Oz-Levi, Marilyn Safran, Doron Lancet
2017 BioMedical Engineering OnLine  
The GeneCards suite databases, which include GeneCards (human genes), MalaCards (human diseases) and PathCards (human pathways) together with additional tools, are presented with the focus on MalaCards  ...  A key challenge in the realm of human disease research is next generation sequencing (NGS) interpretation, whereby identified filtered variant-harboring genes are associated with a patient's disease phenotypes  ...  PathCards: multi- source consolidation of human biological pathways, database [8] GeneLoc Affiliated database Genome locator Rosen et al.  ... 
doi:10.1186/s12938-017-0359-2 pmid:28830434 pmcid:PMC5568599 fatcat:nr5iblpqh5bn5glqnrgelrdehm

pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis

Sara Rahmati, Mark Abovsky, Chiara Pastrello, Igor Jurisica
2016 Nucleic Acids Research  
In order to address all these challenges, we developed pathDIP, which integrates data from 20 source pathway databases, 'core pathways', with physical protein-protein interactions to predict biologically  ...  about underlying physical connectivity of pathway members, and high fraction of protein-coding genes without any pathway annotations, i.e.  ...  One of the major remaining challenges is a comprehensive same-class core pathway consolidation across multiple sources.  ... 
doi:10.1093/nar/gkw1082 pmid:27899558 pmcid:PMC5210562 fatcat:g2ra5celpfbpdfp5gwlloq22rm

VarElect: the phenotype-based variation prioritizer of the GeneCards Suite

Gil Stelzer, Inbar Plaschkes, Danit Oz-Levi, Anna Alkelai, Tsviya Olender, Shahar Zimmerman, Michal Twik, Frida Belinky, Simon Fishilevich, Ron Nudel, Yaron Guan-Golan, David Warshawsky (+9 others)
2016 BMC Genomics  
Next generation sequencing (NGS) provides a key technology for deciphering the genetic underpinnings of human diseases.  ...  Typical NGS analyses of a patient depict tens of thousands non-reference coding variants, but only one or very few are expected to be significant for the relevant disorder.  ...  California (USA), the NHGRI grant U41HG003345 and the Crown Human Genome Center and the Nella and Leon Benoziyo Center for Neurosciences at the Weizmann Institute of Sciences.  ... 
doi:10.1186/s12864-016-2722-2 pmid:27357693 pmcid:PMC4928145 fatcat:zbmio3et65h23phhmmgyve46z4

PathMe: merging and exploring mechanistic pathway knowledge

Daniel Domingo-Fernández, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt, Martin Hofmann-Apitius
2019 BMC Bioinformatics  
The complexity of representing biological systems is compounded by an ever-expanding body of knowledge emerging from multi-omics experiments.  ...  Such a unification of pathway knowledge is imperative in enhancing the comprehension and modeling of biological abstractions.  ...  The funding body did not play a role in the design of the study and collection, analysis, and interpretation of data, or in writing the manuscript.  ... 
doi:10.1186/s12859-019-2863-9 fatcat:vh722vrjrjeexexkl6pri52hs4

Molecular disease presentation in diabetic nephropathy

Andreas Heinzel, Irmgard Mühlberger, Gil Stelzer, Doron Lancet, Rainer Oberbauer, Maria Martin, Paul Perco
2015 Nephrology, Dialysis and Transplantation  
on the level of molecular pathways and processes.  ...  We will also provide concepts on how to integrate findings of these individual studies (i) on the level of functional processes using the gene-ontology vocabulary, (ii) on the level of molecular pathways  ...  The GeneCards system currently holds information on molecular pathways from 12 sources covering a total of 3215 biological pathways and 11 478 unique genes  ... 
doi:10.1093/ndt/gfv267 pmid:26209734 fatcat:umjf3m74wjfg3o4wwbawoyjoge

In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR

Gopal Pawar, Judith C. Madden, David Ebbrell, James W. Firman, Mark T. D. Cronin
2019 Frontiers in Pharmacology  
However, a systematic review and grouping of databases, based on purpose and information content, consolidated in a single source, has been lacking.  ...  ), exposure, omics, pathways, Absorption, Distribution, Metabolism and Elimination (ADME) properties, clinical trials, pharmacovigilance, patents-related databases, biological (genes, enzymes, proteins  ...  Its latest version includes 2,244 human pathways, 12,047 reactions, 10,778 proteins, and 1,948 small molecules. PathCards is an integrated database of human biological pathways and their annotations.  ... 
doi:10.3389/fphar.2019.00561 pmid:31244651 pmcid:PMC6580867 fatcat:t3junhqvxfeslcu37pihztlxiq

Comprehensive network analysis reveals alternative splicing-related lncRNAs in hepatocellular carcinoma [article]

Junqing Wang, Yixin Chen, Keli Xu, Yin-yuan Mo, Yunyun Zhou
2019 bioRxiv   pre-print
We identified a total of 1375 splicing switched isoforms and further analyzed their biological functions.  ...  To model the heterogeneous networks in a single framework, we developed a multi-graphic random walk (RWMG) network method to prioritize the lncRNAs associated with AS in HCC.  ...  Acknowledgements N/A Declaration of Interest The authors declare no potential conflicts of interest.  ... 
doi:10.1101/548263 fatcat:cjfrsyfazzdyrgo47jur5f37qq

Genome analysis and knowledge-driven variant interpretation with TGex

Dvir Dahary, Yaron Golan, Yaron Mazor, Ofer Zelig, Ruth Barshir, Michal Twik, Tsippi Iny Stein, Guy Rosner, Revital Kariv, Fei Chen, Qiang Zhang, Yiping Shen (+3 others)
2019 BMC Medical Genomics  
This is enabled by GeneCards' recently developed GeneHancer, a novel integrative and fully annotated database of human enhancers and promoters.  ...  VarElect leverages the widely used GeneCards knowledgebase, which integrates information from > 150 automatically-mined data sources.  ...  The indirect mode benefits from GeneCards' diverse gene-to-gene data links, including the broad pathway information in PathCards, the Suite's unified pathway database that integrates 12 pathway sources  ... 
doi:10.1186/s12920-019-0647-8 pmid:31888639 pmcid:PMC6937949 fatcat:ixi7j3mqqzflrgzaj5wwwb3xjm

Computational resources associating diseases with genotypes, phenotypes and exposures

Wenliang Zhang, Haiyue Zhang, Huan Yang, Miaoxin Li, Zhi Xie, Weizhong Li
2018 Briefings in Bioinformatics  
He is interested in understanding transcriptional and translational regulation through the integrative analysis of multi-omics data.  ...  Wenliang Zhang is a PhD student in Zhongshan School of Medicine at Sun Yat-sen University. His research is focused on the interpretation of human genotypes and phenotypes.  ...  drugs, clinical candidates, biological pathways and RNA expressions (Table 5 ).  ... 
doi:10.1093/bib/bby071 pmid:30102366 fatcat:63ijmbhgxbf6pousquyuhl3s3a

Common genetic variation drives molecular heterogeneity in human iPSCs

Helena Kilpinen, Angela Goncalves, Andreas Leha, Vackar Afzal, Kaur Alasoo, Sofie Ashford, Sendu Bala, Dalila Bensaddek, Francesco Paolo Casale, Oliver J. Culley, Petr Danecek, Adam Faulconbridge (+31 others)
2017 Nature  
Our study outlines the major sources of genetic and phenotypic variation in iPSCs and establishes their suitability as models of complex human traits and cancer.  ...  Induced pluripotent stem cell (iPSC) technology has enormous potential to provide improved cellular models of human disease.  ...  PathCards: multi-source consolidation of human biological pathways. Database (Oxford) 2015, doi:10.1093/database/bav006 (2015). 24 GTEx Consortium.  ... 
doi:10.1038/nature22403 pmid:28489815 pmcid:PMC5524171 fatcat:fifbiektdvcnvfcohcqrhr277i

Bioinformatics analysis of proteins and proteomes

Islam Mohammad
2022
terms and biochemical pathways of novel organisms, or "missing" proteins.  ...  Despite the presence of the large volume of mass spectrometry (MS) data in various datasets, over 10% human proteins are still considered 'missing'.  ...  The format of this thesis will not permit me to list every one of them. However, I like to acknowledge and thank the following key persons.  ... 
doi:10.25949/19433357 fatcat:idrznpnkmfctfoxypc5cztsn3m

Utility of machine learning approaches for cancer diagnosis and analysis from RNA sequencing

Jasleen K Grewal
2020
In precision oncology, manual analysis of the tumour's genomic profile is used to understand tumour biology and driver pathways.  ...  Molecular data has revealed differences in the genetic makeup of cancers that appear morphologically similar, motivating the use of molecular diagnostics.  ...  Pathway analysis for individual samples Calculation of pathway importance Pathways were curated manually at the Michael Smith Genome Sciences Centre from KEGG [99] , Reactome [45] , PathCards [9]  ... 
doi:10.14288/1.0394043 fatcat:w5s5l4nlb5aylguqosmfcuhami