Job:Open positions at the Center for Molecular Oncology, MSKCC, New York
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6.4 years ago

The CMO is one of several Collaborative Research Centers at MSKCC with the mission to promote precision oncology through large-scale molecular profiling of tumors and correlation to clinical outcomes. This work informs the treatment strategies of oncologists at MSK, providing tangible benefits to patients with complex tumors. Scientists at the CMO collaborate with clinicians and researchers across MSK to understand their work and design sequencing experiments to provide novel insights. This ensures that core skills and experience in sequencing/bioinformatics don't need to be duplicated within each investigator's lab. Conversely, to avoid creating a dependency on us, our tools/pipelines are open-sourced on GitHub [1,2,3,4] and decently documented. Described below are some key groups within the CMO.

Led by Agnes Viale, the Integrated Genomics Operation consists of multiple wet lab teams responsible for sequencing operations, and the Data Team (managed by David McManamon) with Java/Python developers responsible for workflow automation, sample tracking, run-level QC, and FASTQ/BAM delivery.

Led by Nicholas Socci, CMO Informatics includes software engineers (managed by Allan Bolipata) and bioinformatics engineers responsible for portable/modular bioinformatics infrastructure (Python), analysis workflows (CWL/Nextflow), sample-level QC, and publication-ready plots and results for researchers who do not have their own data analysts.

Led by Niki Schultz, Knowledge Systems consists of cancer biologists and Java/Javascript engineers responsible for UIs/APIs that are popular in the cancer research community like the cBioPortal, OncoKB, and oncotree.

Led by Mark Donoghue, CMO Computational Sciences (CCS) is a team of scientists who handle the translational projects that need more nuanced analysis (in R/Python), beyond what can be automated, like allelic imbalance and somatic hotspots.

Led by Mike Berger and managed by Brian Houck-Loomis, Technology Innovation consists of bench scientists and computational biologists developing new assays/techniques for ctDNA, RNA-seq, methyl-seq, and proteins. Ronak Shah manages the team building the MSK-ACCESS ctDNA workflow. Mike is also responsible for MSK-IMPACT, the first NGS assay approved by the FDA for tumor-profiling.

Please visit for a list of open positions at the CMO.

sequencing cancer R python genetics • 7.5k views
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Hi Cyriac, Since this post is modified two days ago, I am wondering if these positions are still open?

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Yes, I try to keep it up to date with what's open/filled. You can also visit and query for "CMO".


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