Publications | Computational Cancer Genomics Lab

selected publications

FFiXR: A Machine Learning Framework for Accurate Somatic Mutation Calling from FFPE RNA-seq data in Cancer

Livne, O., Yizhak, K.

bioRxiv (2025)

A single-Cell Atlas of the Breast Cancer Microenvironment Identifies Subtype-specific Tumor-Immune Landscape and Vulnerabilities

Zisman Schachter, L., Pinhasi, A., Yizhak, K.

bioRxiv (2025)

scXpand: Pan-cancer Detectionof T-cell Clonal Expansion from Single-cell RNA Sequencing Without Paired TCR Sequencing

Shorer, O., Amir, R., Yizhak, K.

bioRxiv (2025)

Immature Monocytic Cells within Tumors Differentiate into Immunosuppressive Cells in Resistant Tumors to Immunotherapy

Levin, S., Benguigui, M., Manobla, B., Buxbaum, C., Raviv, Z., Yizhak, K.* & Shaked, Y.*. *Equal contribution.

iScience (2025)

Unveiling Alternative Splicing Dynamics in Activated T Lymphocytes and Their Implications for Response to Immune Checkpoint Blockade

Zisman, E., Lewis, R., Stern, O., Tzaban, S., Eisenhower, T., Hendrickson, S., Sade-Feldman M., Silberman-Klein, S., Eisenberg, G., Hacohen, N., Yizhak, K.* & Lotem, M.*. *Equal contribution.

iScience (2025)

Uncovering Predictive Gene and Cellular Signatures for Checkpoint Immunotherapy Response through Machine Learning Analysis of Immune Single-Cell RNA-seq Data

Pinhasi, A., Yizhak, K.

npj Precision Oncology (2025)

Single-cell meta-analysis of T cells reveals clonal dynamics of response to checkpoint immunotherapy

Shorer, O., Pinhasi, A., Yizhak, K.

Cell Genomics (2025)

Metabolic predictors of response to immune checkpoint blockade therapy

Shorer, O., Yizhak, K.

iScience (2023)

Estimating tumor mutational burden from RNA-sequencing without a matched-normal sample

Katzir, R., Rodberg, N., Yizhak, K.

Nature Communications (2022) * Picked to feature in the Editor’s Highlights page

RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues

Yizhak, K., Aguet, F., Kim, , Hess, J., Kubler, K., Grimsby J., Frazer, R., Zhang, H., Haradhvala, N., Rosebrock, D., Livitz, D., Li, X., Arich-Landkof, E., Shoresf, N., Stewart, C., Segre, A., Branton, P., Polak, P., Ardlie, K., Getz, G.

Science (2019)

Defining T cell states associated with response to checkpoint immunotherapy in melanoma

Sade-Feldman, M.*, Yizhak, K.*, Bjorgaard, S., Ray, J., De Boer, C., Jenkins, R., Lieb, D., Chen, J., Frederick, D., Barzily-Rokni, M., Freeman, S., Reuben, , Hoover, P., Villani, A., Ivanova, E., Portell, A., Lizotte, P., Aref, A., Eliane, J., Hammond, M., Vitzthum, H., Blackmon, S., Li, B., Gopalakrishnan, V., Reddy, S., Cooper, Z., Paweletz, C., Barbie, D., Stemmer-Rachamimov, A., Flaherty, K., Wargo, J., Boland, G., Sullivan, R., Getz, G., Hacohen, N. *Equal contribution.

Cell (2018)

A joint analysis of transcriptomic and metabolomic data uncovers enhanced enzyme-metabolite coupling in breast cancer

Auslander, N.,* Yizhak, K.,*, Weinstock, A., Budhu, A., Tang, W., Wang, X., Ambs, S., & Ruppin, E. *Equal contribution.

Scientific Reports(2016)

Diversion of aspartate in ASS1-deficient tumors fosters de novo pyrimidine synthesis

Rabinovich, L. Adler, Yizhak, K., A. Sarver, A. Silberman, S., Stettner, N., Sun, Q., Brandis, A., Helbing, D., Korman, S., Itzkovitz, S., Dimmock, D., Ulitsky, I., Nagamani, S., Ruppin, E. & Erez, A.

Nature (2015)