Pharma and Biomarker - Double Strand

Curation of
Public Datasets

Double Strand’s multidisciplinary team of curators, bioinformaticians, and data engineers has deep experience in data cleaning, integration, and harmonization. Our data organization services include:

Cleaning and Curating Data

Creating Custom Ontologies and Controlled Vocabularies

Creating Custom Data Hierarchies

We support pharmaceutical, biotech, and diagnostics companies to organize data for research applications.

Generation of Multi-omics
Datasets for Target Discovery

We leverage our expertise in omics technologies to untangle crucial insights in the fields of oncology, immunology, and drug discovery. We generate single-cell, spatial transcriptomics, and genomics data from clinical samples in our India-based CAP lab. Our accomplishments in this realm include certification as a service provider for 10X Genomics Visium Spatial Transcriptomics workflow.

Building Custom
Bioinformatics Pipelines

We develop custom pipelines for use in drug discovery and oncology research. Our bioinformatics expertise holds us in good stead when it comes to tackling cutting-edge problems in the field. Our solutions span across:

Cell-type deconvolution for single-cell spatial transcriptomics data

Analysis of fragmentomics data

Early cancer detection and development

Refactoring

Optimizing

Benchmarking algorithms for secondary analysis toolkits

Frequently Asked
Questions

Strand’s data harmonization process ensures that large datasets are handled in a timely and accurate manner, significantly improving efficiency. Our hierarchical structure organizes data from diseases to core data, making it easily navigable. We successfully harmonized over 500 datasets and implemented this structure for a top 20 pharmaceutical company in the US. This included a variety of data types, such as metadata files, raw data and processed data of various types, and post-analysis files.

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Absolutely. Strand’s multidisciplinary team of curators, bioinformaticians, and data engineers work together to harmonize heterogeneous data. Our process includes standardizing terminologies, building NLP-powered dictionaries, and creating custom ontologies to resolve inconsistencies.

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Strand’s expert curators, with deep domain knowledge and extensive experience across multiple modalities, meticulously generate gold-standard datasets. This resolves ambiguities and inconsistencies in biomedical terminology, essential for the accurate extraction of relationships between entities.

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Our client, a diagnostics company, required an NLP algorithm for extracting molecular or genetic data from somatic cancer publications. Strand’s team of curators and reviewers annotated entities and relationships pertaining to genes, diseases, biomarkers, and more for over 1,000 excerpts using brat, an open-source tool. As a result, we delivered a meticulously annotated ground-truth dataset for benchmarking the client’s NLP algorithm.

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Strand’s researchers have evaluated various state-of-the-art and novel methods and developed an end-to-end bioinformatics pipeline that is optimized for speed and robustness.
The main processes in the pipelines such as clustering analysis and cell type annotation were optimized through a systematic evaluation of publicly available tools and databases.

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Frequently Asked
Questions

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Frequently Asked Questions

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Frequently Asked
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