About Me

Years of experience in bioinformatics research and development

I studied Medical Sciences at the University of Tel-Aviv, and completed a PhD under the supervision of Professor Dafna Benayahu. Mythesis explored the bioinformatics of mesenchymal stem cells and tissues. I then spent a post-doc at Columbia University, NY, focusing on the network biology of cancer. My work at Columbia University focused on integrating copy number and gene expression in a probabilistic network to identify novel regulators of melanoma and glioblastoma behavior.

After my post-doc, I spent some years as a group leader at McGill University, focusing on integrating metabolism and expression, and had many fruitful collaborations with experimental (wet) biologists there. 

My corporate duties invovled designing, developing and reviewing a pipeline focused on characterizing DNA variants and mutations in cancer. This role taught me more about programming within a regulatory framework, and how to deal with private patient health data. 

See my LinkedIn profile for more info, or my Google Scholar for publications.

Let's get in touch
Email me, or schedule an initial consultation about your project.
Services

Experimental Design
What kind of data would a bioinformatician need to answer your questions. Which method, how many repeats, to fit your budget.

Dataset analysis from reads to figures 
Going from raw reads (FASTQ files) to identifying mutations (DNA-seq), differentially expressed genes and pathways (RNA-seq/proteomics).  

Interpertation of gene lists and regulatory analysis
What do the results mean functionally and biologically? Are they linked to a pathway or transcription factors? Gene network construction and machine learning to dive into your data. Literature review and comparison to published datasets.

Multi-omic integration
Identifying biological phenomena that are present on multiple levels (DNA, RNA, protein, metabolomics).

Software/pipeline development
If you’ve got a piece of software written by someone (who’s left the lab), I’d be happy to modernize and update it for you. Pipeline construction from scratch in Nextflow to fit your cloud or HPC environment.

Patents

US Patent Application No. 18/747,597, “Method for Selective Sequencing of Cancer DNA,” filed June 19, 2024. Patent Pending
https://patents.google.com/patent/US20240425930A1/

PCT patent application PCT/US2025/055399, “Methods and Systems for Analyzing Low-Input Samples”, filed 15 November 2024, Patent Pending 

Example Publications
  1. Roche PJR, Gytz H, Hussain F, Liang Y, Stub Laursen N, Andersen KR, Nagar B, Akavia UD. Receptor Mediated Delivery of Cas9-Nanobody Induces Cisplatin Synthetic Dose Sensitivity. Biorxiv DOI: 10.1101/389122
  2. Roche PJR, Gytz, H, Hussain F, Cameron CJF, Paquette D, Blanchette M, Dostie J, Nagar B, Akavia UD. Double-Stranded Biotinylated Donor Enhances Homology-Directed Repair in Combination with Cas9 Monoavidin in Mammalian Cells. CRISPR Journal 1, 414-430 (2018)
  3. Arabzadeh A, McGregor K, Breton V, Van Der Kraak L, Akavia UD, Greenwood CMT, Beauchemin N. EphA2 signaling is impacted by carcinoembryonic antigen cell adhesion molecule 1-L expression in colorectal cancer liver metastasis in a cell context-dependent manner. Oncotarget 8, 104330-46 (2017)
  4. Arabzadeh A, Dupaul-Chicoine J, Breton V, Haftchenary S, Yumeen S, Turbide C, Saleh M, McGregor K, Greenwood CM, Akavia UD, Blumberg RS, Gunning PT, Beauchemin N. Carcinoembryonic Antigen Cell Adhesion Molecule 1 long isoform modulates malignancy of poorly differentiated colon cancer cells. Gut 65, 821-9 (2016)
  5. Sanchez-Garcia F*, Villagrasa P*, Matsui J, Kotliar D, Castro V, Akavia UD, Chen B.J, Saucedo-Cuevas L, Barrueco R.R, Llobet-Navas D, Silva J.M.**, Pe’er D**. Integration of Genomic Data Enables Selective Discovery of Breast Cancer Drivers. Cell 159, 1461-75 (2014)
    * Equal Contributions  ** Co-last authors
  6. McGuirk S, Gravel SP, Deblois G, Papadopoli D, Faubert B, Wegner A, Hiller K, Avizonis D, Akavia UD, Jones R.G, Giguère V, St-Pierre J. PGC-1alpha supports glutamine metabolism in breast cancer. Cancer & Metabolism 1, 22 (2013)
  7. Becker-Weimann S, Xiong G, Furuta S, Han J, Kuhn I, Akavia UD, Pe’er D, Bissell M.J, Xu R. NFkB disrupts tissue polarity in 3D by preventing integration of microenvironmental signals. Oncotarget 4, 2010-2020 (2013)
  8. Danussi, C*, Akavia, UD*, Niola F, Jovic A, Lasorella A, Pe’er D**, Iavarone, A**. RHPN2 Drives Mesenchymal Transformation in Malignant Glioma by Triggering RhoA Activation. Cancer Research 73, 5140–50 (2013)
    *Equal Contributions  ** Co-last authors
  9. Wolpaw A.J, Shimada K, Skouta R, Welsch M.E, Akavia UD, Pe’er D, Shaik F, Bulinski J.C, Stockwell B.R. Modulatory profiling identifies mechanisms of small molecule-induced cell death. PNAS 108, E771-E780 (2011)
  10. Akavia, UD*, Litvin O*, Kim J, Sanchez-Garcia F, Kotliar D, Causton H.C, Pochanard P, Mozes E, Garraway L.A, Pe’er D. An Integrated Approach to Uncover Drivers of Cancer. Cell 143, 1005-1017 (2010)
     *Equal Contributions