Malwina Prater

Bioinformatics.

I am a bioinformatician and data scientist with 9 years of experience in collaborative research and NGS data analysis. With deep and extensive experience in scientific research and bioinformatics, I am uniquely positioned to integrate and consult on both areas of wet lab and dry lab research. My passion is seeing scientific advances benefiting the world.

In my current role as Senior Data Scientist at Altos Labs, I work across spatial transcriptomics and CRISPR functional genomics, and build the pipelines and infrastructure that let teams run them at scale. Among my responsibilities are:

  • Building spatial transcriptomics (Xenium) QC infrastructure in the nf-xenium-processing pipeline: an SNR and focus-quality module, redesigned image and molecule QC reports, multi-stain tissue-extent segmentation masks, and metric drift analysis and cross-cohort calibration to gate high-quality slides into downstream machine-learning analysis
  • Developing CRISPR screen infrastructure: migrating the CRISPRlibQC pipeline from a command-line tool to a Seqera pipeline, optimised for speed and memory to scale to whole-genome guide design, and building interactive dashboards for visualisation, filtering and reporting
  • Delivering guide design and selection across CRISPRa / CRISPRi / knockout modalities, plus screen-design tooling for FACS, colony-forming-efficiency (CFE) and viability screens
  • Acting as a key point of contact for teams running CRISPR screens — advising on experimental design, controls and analysis strategy, and troubleshooting from planning through to interpreting results
  • Contributing Xenium spatial analysis to a manuscript revision
  • Engineering and infrastructure: Nextflow / Seqera pipeline development and compute-environment tuning, containerisation with Docker and image management via AWS ECR, and work on HPC and AWS

Previously, as a Senior Bioinformatician at the Functional Genomics Centre, Cancer Research Horizons (Cambridge, UK), I led a single-cell (Perturb-seq) project portfolio, line-managed and recruited for the bioinformatics team, and managed multiple CRISPR projects, working closely with wet lab scientists and stakeholders on experimental design, pipelines and delivery. I established new CRISPR screen capabilities, ran lethality, isogenic, epigenetic, gene-tiling and in-vivo CRISPR screen analyses, and contributed to the development and deployment of bioinformatic solutions on AWS.

Before that, I provided bioinformatics expertise to Patrick Chinnery’s group at the MRC Mitochondrial Biology Unit, University of Cambridge. My work there focused on exploring and in-depth analysis of single-cell RNA-seq, CROP-seq and MultiOme (scRNA-seq + ATAC-seq) datasets, as well as writing a Nextflow pipeline for single-cell multiome CROP-seq processing.

I am excited about collaborative science, data integration and visualisation.