Data Analysis and Consultation

Our dedicated bioinformatics staff have deep expertise in a broad range of sequence-based assays. We tailor our level of engagement to each project’s needs, from helping to troubleshoot code to collaborating on development of complex novel workflows. Our team helps scientists tackle projects of varying complexity, from small pilot runs to surveys of hundreds of specimens analyzed via multiple assays.

Typical supported workflows include whole exome sequencing, targeted amplicon sequencing, somatic variant calling, CRISPR/Cas9 knockout analysis, bulk RNA-seq expression profiling, single-cell expression profiling, and single-cell immune repertoire sequencing. We also analyze epigenomic profiling data and can help users compare these profiles with RNA-seq expression data when available. For more information about our standard workflows, please consult the bioinformatics services of the Genomics & Bioinformatics shared resource.

In addition to focused, shorter-duration projects, we often work with researchers to bring new techniques to the center and to engage in longer-term collaborative work. Larger specialized projects we have contributed to recently include: 

• Development of neoantigen-profiling workflows
• Assembly of a large, disease-specific, gene expression compendium 
• Long-range haplotype phasing
• Development of new methods to profile translational control
• De novo assembly of small viral genomes

For further information about the bioinformatics services we offer, or to schedule a consultation, please email bioinformatics@fredhutch.org.

Modern imaging systems provide an unprecedented capability to observe biological structures, but the size, depth and complexity of these image datasets challenge even top-rated commercial image analysis software. 

Our dedicated scientific staff can assist in developing customized image analysis pipelines and algorithms. Our expertise allows us to create the flexible, sophisticated and high-throughput analysis workflows needed to analyze rich imaging datasets by combining data I/O, image pre-processing, image segmentation and feature extraction, metrics collection, display and export.

We also provide consultation to help select the most appropriate imaging techniques and to plan post-acquisition analyses. We work closely with colleagues in the Cellular Imaging shared resource throughout planning and image acquisition to ensure a seamless transfer of data from instruments to our analysis resources. 

We perform analysis on a wide range of data types generated by light or electron microscopy, including 2D images, 3D stacks and time series. Example metrics for which we have developed versatile quantitative pipelines include cell/object counting, subcellular localization, signal colocalization, cell tracking and spatial distribution, including crowding or neighbor occupancy. Please see the Cellular Imaging shared resource’s image analysis page for more information.

For further information or to schedule consultation please contact Dr. Julien Dubrulle, image analysis staff scientist in the Cellular Imaging core.

Our bioinformatics staff have considerable experience analyzing proteomics data and are available to assist with downstream analysis for various mass spectrometry-based techniques. In close partnership with members of the Proteomics & Metabolomics shared resource, bioinformatics staff have developed custom deconvolution methods for labeled peptides, helped identify long-lived proteins in yeast through analysis of metabolically labeled peptides, searched for specific secondary structure motifs in the proteomes of non-model organisms, and taught introductory courses on the interpretation of tandem mass spectra.

For assistance analyzing proteomics data please contact Dr. Chenwei Lin, staff scientist in the Proteomics & Metabolomics core.