Selected Publications
Wander, S.A., Cohen, O., Gong, X., Johnson, G.N., Buendia-Buendia, J.E., Lloyd, M.R., Kim, D., Luo, F., Mao, P., Helvie, K. and Kowalski, K.J., 2020. The genomic landscape of intrinsic and acquired resistance to cyclin-dependent kinase 4/6 inhibitors in patients with hormone receptor–positive metastatic breast cancer. Cancer discovery, 10(8), pp.1174-1193.
Nayar, U., Cohen, O., Kapstad, C., Cuoco, M.S., Waks, A.G., Wander, S.A., Painter, C., Freeman, S., Persky, N.S., Marini, L. and Helvie, K., 2019. Acquired HER2 mutations in ER+ metastatic breast cancer confer resistance to estrogen receptor–directed therapies. Nature genetics, 51(2), pp.207-216.
Mao, P., Cohen, O., Kowalski, K.J., Kusiel, J.G., Buendia-Buendia, J.E., Cuoco, M.S., Exman, P., Wander, S.A., Waks, A.G., Nayar, U. and Chung, J., 2020. Acquired FGFR and FGF alterations confer resistance to estrogen receptor (ER) targeted therapy in ER+ metastatic breast cancer. Clinical Cancer Research, 26(22), pp.5974-5989.
Waks, A.G., Cohen, O., Kochupurakkal, B., Kim, D., Dunn, C.E., Buendia, J.B., Wander, S., Helvie, K., Lloyd, M.R., Marini, L. and Hughes, M.E., 2020. Reversion and non-reversion mechanisms of resistance to PARP inhibitor or platinum chemotherapy in BRCA1/2-mutant metastatic breast cancer. Annals of Oncology, 31(5), pp.590-598.
Sklarz, M., Levin, L., Gordon, M. and Chalifa-Caspi, V., 2017. NeatSeq-Flow: a lightweight high throughput sequencing workflow platform for non-programmers and programmers alike. BioRxiv, p.173005.
Cohen, O., Doron, S., Wurtzel, O., Dar, D., Edelheit, S., Karunker, I., Mick, E. and Sorek, R., 2016. Comparative transcriptomics across the prokaryotic tree of life. Nucleic Acids Research, 44(W1), pp.W46-W53.
Cohen, O., Gophna, U. and Pupko, T., 2011. The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Molecular biology and evolution, 28(4), pp.1481-1489.
Latest publications
Klughammer, J., Abravanel, D.L., Segerstolpe, Å., Blosser, T.R., Goltsev, Y., Cui, Y., Goodwin, D.R., Sinha, A., Ashenberg, O., Slyper, M. and Vigneau, S., 2024. A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features. Nature Medicine, 30(11), pp.3236-3249.
AbuMadighem, A., Cohen, O., and Huleihel, M.. 2024. Elucidating the Transcriptional States of Spermatogenesis—Joint Analysis of Germline and Supporting Cell, Mice and Human, Normal and Perturbed, Bulk and Single-Cell RNA-Seq. Biomolecules 14, no. 7: 840.
Kaufman, B., Taha, T., Abramov, O., Zohar, Y., Mhameed, K., Cohen, O., Porgador, A., Elkabets, M. and Billan, S. 2024. PD1 ligand functionality a biomarker of response to anti PD1 treatment in patients with HNSCC. NPJ Precision Oncology, 8(1), p.126.
Fu, X., Pereira, R., Liu, C.C., De Angelis, C., Shea, M.J., Nanda, S., Qin, L., Mitchell, T., Cataldo, M.L., Veeraraghavan, J. and Sethunath, V., 2023. High FOXA1 levels induce ER transcriptional reprogramming, a pro-metastatic secretome, and metastasis in endocrine-resistant breast cancer. Cell Reports, 42(8).
Kaufman, B., Abramov, O., Ievko, A., Apple, D., Shlapobersky, M., Allon, I., Greenshpan, Y., Bhattachrya, B., Cohen, O., Charkovsky, T. and Gayster, A., 2023. Functional binding of PD1 ligands predicts response to anti-PD1 treatment in patients with cancer. Science advances, 9(21), p.eadg2809.
Jagadeeshan, S., Prasad, M., Badarni, M., Ben-Lulu, T., Liju, V.B., Mathukkada, S., Saunders, C., Shnerb, A.B., Zorea, J., Yegodayev, K.M., Wainer, M., Vtorov, L., Allon, I., Cohen, O., Gausdal, G., Friedmann-Morvinski, D., Cheong, S.C., Ho, A.L., Rosenberg, A.J., Kessler, L., Burrows, F., Kong, D., Grandis, J.R., Gutkind, J.S. and Elkabets, M., 2023. Mutated HRAS activates YAP1–AXL signaling to drive metastasis of head and neck cancer. Cancer research, 83(7), pp.1031-1047.