Sasan Hashemi

Sasan Hashemi

Carmel, Indiana, United States
393 followers 388 connections

Activity

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Experience

  • Kayhan Space Graphic
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    Indianapolis, Indiana, United States

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    San Francisco Bay Area

Education

  • Indiana University

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    Activities and Societies: HASTAC, Indy Big Data

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    Activities and Societies: METU-BIN iGEM

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Licenses & Certifications

Publications

  • A framework for identifying genotypic information from clinical records: exploiting integrated ontology structures to transfer annotations between ICD codes and Gene Ontologies

    IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

    Although some methods are proposed for automatic ontology generation, none of them address the issue of integrating large-scale heterogeneous biomedical ontologies. We propose a novel approach for integrating various types of ontologies efficiently and apply it to integrate International Classification of Diseases, Ninth Revision, Clinical Modification (ICD9CM) and Gene Ontologies (GO). This approach is one of the early attempts to quantify the associations among clinical terms (e.g. ICD9…

    Although some methods are proposed for automatic ontology generation, none of them address the issue of integrating large-scale heterogeneous biomedical ontologies. We propose a novel approach for integrating various types of ontologies efficiently and apply it to integrate International Classification of Diseases, Ninth Revision, Clinical Modification (ICD9CM) and Gene Ontologies (GO). This approach is one of the early attempts to quantify the associations among clinical terms (e.g. ICD9 codes) based on their corresponding genomic relationships. We reconstructed a merged tree for a partial set of GO and ICD9 codes and measured the performance of this tree in terms of associations’ relevance by comparing them with two well-known disease-gene datasets (i.e. MalaCards and Disease Ontology). Furthermore, we compared the genomic-based ICD9 associations to temporal relationships between them from electronic health records. Our analysis shows promising associations supported by both comparisons suggesting a high reliability. We also manually analyzed several significant associations and found promising support from literature.

    Other authors
    • Ran Xia
    • Yang Xiang
    • Sarath Chandra Janga
    See publication
  • Database of RNA binding protein expression and disease dynamics (READ DB).

    Oxford Database

    RNA Binding Protein (RBP) Expression and Disease Dynamics database (READ DB) is a non-redundant, curated database of human RBPs. RBPs curated from different experimental studies are reported with their annotation, tissue-wide RNA and protein expression levels, evolutionary conservation, disease associations, protein-protein interactions, microRNA predictions, their known RNA recognition sequence motifs as well as predicted binding targets and associated functional themes, providing a one stop…

    RNA Binding Protein (RBP) Expression and Disease Dynamics database (READ DB) is a non-redundant, curated database of human RBPs. RBPs curated from different experimental studies are reported with their annotation, tissue-wide RNA and protein expression levels, evolutionary conservation, disease associations, protein-protein interactions, microRNA predictions, their known RNA recognition sequence motifs as well as predicted binding targets and associated functional themes, providing a one stop portal for understanding the expression, evolutionary trajectories and disease dynamics of RBPs in the context of post-transcriptional regulatory networks.

    Other authors
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  • The human RBPome: From genes and proteins to human disease

    RNA binding proteins (RBPs) play a central role in mediating post transcriptional regulation of genes. However less is understood about them and their regulatory mechanisms. In this study, we construct a catalogue of 1344 experimentally confirmed RBPs. The domain architecture of RBPs enabled us to classify them into three groups - Classical (29%), Non-classical (19%) and unclassified (52%). A higher percentage of proteins with unclassified domains reveals the presence of various uncharacterised…

    RNA binding proteins (RBPs) play a central role in mediating post transcriptional regulation of genes. However less is understood about them and their regulatory mechanisms. In this study, we construct a catalogue of 1344 experimentally confirmed RBPs. The domain architecture of RBPs enabled us to classify them into three groups - Classical (29%), Non-classical (19%) and unclassified (52%). A higher percentage of proteins with unclassified domains reveals the presence of various uncharacterised motifs that can potentially bind RNA. RBPs were found to be highly disordered compared to Non-RBPs (p<2.2e-16, Fisher's exact test), suggestive of a dynamic regulatory role of RBPs in cellular signalling and homeostasis. Evolutionary analysis in 62 different species showed that RBPs are highly conserved compared to Non-RBPs (p<2.2e-16, Wilcox-test), reflecting the conservation of various biological processes like mRNA splicing and ribosome biogenesis. The expression patterns of RBPs from human proteome map revealed that ~40% of them are ubiquitously expressed and ~60% are tissue-specific. RBPs were also seen to be highly associated with several neurological disorders, cancer and inflammatory diseases. Anatomical contexts like B cells, T-cells, foetal liver and foetal brain were found to be strongly enriched for RBPs, implying a prominent role of RBPs in immune responses and different developmental stages. The catalogue and meta-analysis presented here should form a foundation for furthering our understanding of RBPs and the cellular networks they control, in years to come

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  • Large-scale signaling network reconstruction

    IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

    Reconstructing the topology of a signaling network by means of RNA interference (RNAi) technology is an underdetermined problem especially when a single gene in the network is knocked down or observed. In addition, the exponential search space limits the existing methods to small signaling networks of size 10-15 genes. In this paper, we propose integrating RNAi data with a reference physical interaction network. We formulate the problem of signaling network reconstruction as finding the minimum…

    Reconstructing the topology of a signaling network by means of RNA interference (RNAi) technology is an underdetermined problem especially when a single gene in the network is knocked down or observed. In addition, the exponential search space limits the existing methods to small signaling networks of size 10-15 genes. In this paper, we propose integrating RNAi data with a reference physical interaction network. We formulate the problem of signaling network reconstruction as finding the minimum number of edit operations on a given reference network. The edit operations transform the reference network to a network that satisfies the RNAi observations. We show that using a reference network does not simplify the computational complexity of the problem. Therefore, we propose two methods which provide near optimal results and can scale well for reconstructing networks up to hundreds of components. We validate the proposed methods on synthetic and real data sets. Comparison with the state of the art on real signaling networks shows that the proposed methodology can scale better and generates biologically significant results.

    Other authors
    • Eyup Serdar Ayaz
    • Yusuf Kavurucu
    • Tolga Can
    • Tamer Kahveci
    See publication

Languages

  • English

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  • Persian

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  • Azerbaijani

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  • Turkish

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