Hiring: Scientific Lead, Molecular Characterization Company: BioSpace Location: New York, NY Job Posted Time: 2026-09-13 10:27:29 Employment Type: Contract Target Skills & Keywords : Python About the job Experience: •3+ years of hands-on research or platform development experience in an academic or industry setting. Required Skills: •Design and lead the development of spatial transcriptomics and multi-modal spatial workflows, encompassing tissue optimization, library construction, and end-to-end data generation using platforms such as Visium HD, CosMx, and Xenium. •Strategically drive integration of spatial transcriptomics with complementary modalities, including spatial proteomics (e.g., CosMx protein panels, CODEX/PhenoCycler) and single-cell data, to generate comprehensive tissue-level molecular maps. •Establish and continuously improve tissue processing standards for diverse sample types relevant to Oncology (FFPE, fresh-frozen, bone marrow, cryosections), with a focus on maximizing data quality from challenging or low-input specimens. •Develop image analysis pipelines in collaboration with discovery informatics, including tissue segmentation, cell type deconvolution, and morphological co-registration using tools such as QuPath, HALO, or equivalent platforms. •Evaluate emerging spatial technologies on an ongoing basis and translate promising platforms into internal capabilities through systematic feasibility assessment and implementation planning. •Scale long-read sequencing workflows (PacBio and Oxford Nanopore) for applications including structural variant detection, isoform characterization, epigenetic sequencing (e.g., methylation, Fiber-seq), and custom targeted approaches. •Contribute to automation of NGS and spatial library preparation protocols in collaboration with automation and histology specialists. •Develop custom targeted panels and probe/index designs for the spatial platforms to address specific genomic and transcriptomic questions posed by Oncology project teams. Qualifications: •PhD in molecular biology, genomics, genetics, or a closely related discipline, with 3+ years of hands-on research or platform development experience in an academic or industry setting. •Deep hands-on expertise in spatial transcriptomics platforms (Visium HD, CosMx, Xenium, or equivalent), from tissue section preparation through library construction and QC. •Demonstrated experience with tissue optimization and sample handling for spatial applications across diverse and challenging sample types (FFPE, fresh-frozen, bone marrow, cryosections). •Operational familiarity with long-read sequencing platforms (Oxford Nanopore and/or PacBio); hands-on experience with library construction, QC, and data interpretation is a strong plus. •Proven experience automating NGS or spatial library preparation workflows using liquid handling platforms (e.g., Hamilton, Beckman Coulter, or equivalent). •Solid functional working knowledge of spatial data analysis tools (e.g., Seurat, Squidpy, Scanpy) and image analysis platforms (e.g., QuPath, HALO) for tissue-based data. •Proficiency scripting in Python and/or R to apply, adapt, and troubleshoot single-cell and spatial analysis tools (e.g., Scanpy/Squidpy, Seurat). •Demonstrated track record of building or deploying new molecular platforms or technologies, not solely operating established protocols. •Broad NGS experience including RNA-seq, WES, single-cell sequencing, and epigenetic profiling (ATAC-seq, bisulfite sequencing, or equivalent). •Excellent scientific communication skills; ability to convey complex results clearly to technical and non-technical stakeholders. Interested candidates, please apply directly through the job posting on company's career page or try via AI auto apply on this platform. Don't miss this opportunity to join a forward-thinking team!