Matan Hofree

2024

Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy

Chen, J. H., Nieman, L. T., Spurrell, M., Jorgji, V., Elmelech, L., Richieri, P., Xu, K. H., Madhu, R., Parikh, M., Zamora, I., Mehta, A., Nabel, C. S., Freeman, S. S., Pirl, J. D., Lu, C., Meador, C. B., Barth, J. L., Sakhi, M., Tang, A. L. & Sarkizova, S. & 17 others, Price, C., Fernandez, N. F., Emanuel, G., He, J., Van Raay, K., Reeves, J. W., Yizhak, K., Hofree, M., Shih, A., Sade-Feldman, M., Boland, G. M., Pelka, K., Aryee, M. J., Mino-Kenudson, M., Gainor, J. F., Korsunsky, I. & Hacohen, N., Apr 2024, In: Nature Immunology. 25, 4, p. 644-658 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

38 Scopus citations

Senescence of human pancreatic beta cells enhances functional maturation through chromatin reorganization and promotes interferon responsiveness

Patra, M., Klochendler, A., Condiotti, R., Kaffe, B., Elgavish, S., Drawshy, Z., Avrahami, D., Narita, M., Hofree, M., Drier, Y., Meshorer, E., Dor, Y. & Ben-Porath, I., 24 Jun 2024, In: Nucleic Acids Research. 52, 11, p. 6298-6316 19 p.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

Senescent cancer-associated fibroblasts in pancreatic adenocarcinoma restrict CD8⁺ T cell activation and limit responsiveness to immunotherapy in mice

Assouline, B., Kahn, R., Hodali, L., Condiotti, R., Engel, Y., Elyada, E., Mordechai-Heyn, T., Pitarresi, J. R., Atias, D., Steinberg, E., Bidany-Mizrahi, T., Forkosh, E., Katz, L. H., Benny, O., Golan, T., Hofree, M., Stewart, S. A., Atlan, K. A., Zamir, G. & Stanger, B. Z. & 2 others, Berger, M. & Ben-Porath, I., Dec 2024, In: Nature Communications. 15, 1, 6162.

Research output: Contribution to journal › Article › peer-review

Open Access

9 Scopus citations

2023

Efficacy and safety of metabolic interventions for the treatment of severe COVID-19: in vitro, observational, and non-randomized open-label interventional study

Ehrlich, A., Ioannidis, K., Nasar, M., Abu Alkian, I., Daskal, Y., Atari, N., Kliker, L., Rainy, N., Hofree, M., Shafran Tikva, S., Houri, I., Cicero, A., Pavanello, C., Sirtori, C. R., Cohen, J. B., Chirinos, J. A., Deutsch, L., Cohen, M., Gottlieb, A. & Bar-Chaim, A. & 4 others, Shibolet, O., Mandelboim, M., Maayan, S. L. & Nahmias, Y., 27 Jan 2023, In: eLife. 12

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

Multimodal single-cell and whole-genome sequencing of small, frozen clinical specimens

Wang, Y., Fan, J. L., Melms, J. C., Amin, A. D., Georgis, Y., Barrera, I., Ho, P., Tagore, S., Abril-Rodríguez, G., He, S., Jin, Y., Biermann, J., Hofree, M., Caprio, L., Berhe, S., Khan, S. A., Henick, B. S., Ribas, A., Macosko, E. Z. & Chen, F. & 5 others, Taylor, A. M., Schwartz, G. K., Carvajal, R. D., Azizi, E. & Izar, B., Jan 2023, In: Nature Genetics. 55, 1, p. 19-25 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

27 Scopus citations

2022

Genome-wide CRISPR screen identifies PRC2 and KMT2D-COMPASS as regulators of distinct EMT trajectories that contribute differentially to metastasis

Zhang, Y., Donaher, J. L., Das, S., Li, X., Reinhardt, F., Krall, J. A., Lambert, A. W., Thiru, P., Keys, H. R., Khan, M., Hofree, M., Wilson, M. M., Yedier-Bayram, O., Lack, N. A., Onder, T. T., Bagci-Onder, T., Tyler, M., Tirosh, I., Regev, A. & Lees, J. A. & 1 others, Weinberg, R. A., Apr 2022, In: Nature Cell Biology. 24, 4, p. 554-564 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

68 Scopus citations

Mouse fetal growth restriction through parental and fetal immune gene variation and intercellular communications cascade

Kaur, G., Porter, C. B. M., Ashenberg, O., Lee, J., Riesenfeld, S. J., Hofree, M., Aggelakopoulou, M., Subramanian, A., Kuttikkatte, S. B., Attfield, K. E., Desel, C. A. E., Davies, J. L., Evans, H. G., Avraham-Davidi, I., Nguyen, L. T., Dionne, D. A., Neumann, A. E., Jensen, L. T., Barber, T. R. & Soilleux, E. & 5 others, Carrington, M., McVean, G., Rozenblatt-Rosen, O., Regev, A. & Fugger, L., Dec 2022, In: Nature Communications. 13, 1, 4398.

Research output: Contribution to journal › Article › peer-review

Open Access

11 Scopus citations

2021

Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps

Chen, B., Scurrah, C. R., McKinley, E. T., Simmons, A. J., Ramirez-Solano, M. A., Zhu, X., Markham, N. O., Heiser, C. N., Vega, P. N., Rolong, A., Kim, H., Sheng, Q., Drewes, J. L., Zhou, Y., Southard-Smith, A. N., Xu, Y., Ro, J., Jones, A. L., Revetta, F. & Berry, L. D. & 32 others, Niitsu, H., Islam, M., Pelka, K., Hofree, M., Chen, J. H., Sarkizova, S., Ng, K., Giannakis, M., Boland, G. M., Aguirre, A. J., Anderson, A. C., Rozenblatt-Rosen, O., Regev, A., Hacohen, N., Kawasaki, K., Sato, T., Goettel, J. A., Grady, W. M., Zheng, W., Washington, M. K., Cai, Q., Sears, C. L., Goldenring, J. R., Franklin, J. L., Su, T., Huh, W. J., Vandekar, S., Roland, J. T., Liu, Q., Coffey, R. J., Shrubsole, M. J. & Lau, K. S., 22 Dec 2021, In: Cell. 184, 26, p. 6262-6280.e26

Research output: Contribution to journal › Article › peer-review

Open Access

164 Scopus citations

Implications of intratumor heterogeneity on consensus molecular subtype (Cms) in colorectal cancer

Chowdhury, S., Hofree, M., Lin, K., Maru, D., Kopetz, S. & Shen, J. P., 1 Oct 2021, In: Cancers. 13, 19, 4923.

Research output: Contribution to journal › Article › peer-review

Open Access

17 Scopus citations

Spatially organized multicellular immune hubs in human colorectal cancer

Pelka, K., Hofree, M., Chen, J. H., Sarkizova, S., Pirl, J. D., Jorgji, V., Bejnood, A., Dionne, D., Ge, W. H., Xu, K. H., Chao, S. X., Zollinger, D. R., Lieb, D. J., Reeves, J. W., Fuhrman, C. A., Hoang, M. L., Delorey, T., Nguyen, L. T., Waldman, J. & Klapholz, M. & 52 others, Wakiro, I., Cohen, O., Albers, J., Smillie, C. S., Cuoco, M. S., Wu, J., Su, M. J., Yeung, J., Vijaykumar, B., Magnuson, A. M., Asinovski, N., Moll, T., Goder-Reiser, M. N., Applebaum, A. S., Brais, L. K., DelloStritto, L. K., Denning, S. L., Phillips, S. T., Hill, E. K., Meehan, J. K., Frederick, D. T., Sharova, T., Kanodia, A., Todres, E. Z., Jané-Valbuena, J., Biton, M., Izar, B., Lambden, C. D., Clancy, T. E., Bleday, R., Melnitchouk, N., Irani, J., Kunitake, H., Berger, D. L., Srivastava, A., Hornick, J. L., Ogino, S., Rotem, A., Vigneau, S., Johnson, B. E., Corcoran, R. B., Sharpe, A. H., Kuchroo, V. K., Ng, K., Giannakis, M., Nieman, L. T., Boland, G. M., Aguirre, A. J., Anderson, A. C., Rozenblatt-Rosen, O., Regev, A. & Hacohen, N., 2 Sep 2021, In: Cell. 184, 18, p. 4734-4752.e20

Research output: Contribution to journal › Article › peer-review

Open Access

375 Scopus citations

2020

A Distinct Transcriptional Program in Human CAR T Cells Bearing the 4-1BB Signaling Domain Revealed by scRNA-Seq

Boroughs, A. C., Larson, R. C., Marjanovic, N. D., Gosik, K., Castano, A. P., Porter, C. B. M., Lorrey, S. J., Ashenberg, O., Jerby, L., Hofree, M., Smith-Rosario, G., Morris, R., Gould, J., Riley, L. S., Berger, T. R., Riesenfeld, S. J., Rozenblatt-Rosen, O., Choi, B. D., Regev, A. & Maus, M. V., 2 Dec 2020, In: Molecular Therapy. 28, 12, p. 2577-2592 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

63 Scopus citations

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

Slyper, M., Porter, C. B. M., Ashenberg, O., Waldman, J., Drokhlyansky, E., Wakiro, I., Smillie, C., Smith-Rosario, G., Wu, J., Dionne, D., Vigneau, S., Jané-Valbuena, J., Tickle, T. L., Napolitano, S., Su, M. J., Patel, A. G., Karlstrom, A., Gritsch, S., Nomura, M. & Waghray, A. & 30 others, Gohil, S. H., Tsankov, A. M., Jerby-Arnon, L., Cohen, O., Klughammer, J., Rosen, Y., Gould, J., Nguyen, L., Hofree, M., Tramontozzi, P. J., Li, B., Wu, C. J., Izar, B., Haq, R., Hodi, F. S., Yoon, C. H., Hata, A. N., Baker, S. J., Suvà, M. L., Bueno, R., Stover, E. H., Clay, M. R., Dyer, M. A., Collins, N. B., Matulonis, U. A., Wagle, N., Johnson, B. E., Rotem, A., Rozenblatt-Rosen, O. & Regev, A., 1 May 2020, In: Nature Medicine. 26, 5, p. 792-802 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

408 Scopus citations

Emergence of a High-Plasticity Cell State during Lung Cancer Evolution

Marjanovic, N. D., Hofree, M., Chan, J. E., Canner, D., Wu, K., Trakala, M., Hartmann, G. G., Smith, O. C., Kim, J. Y., Evans, K. V., Hudson, A., Ashenberg, O., Porter, C. B. M., Bejnood, A., Subramanian, A., Pitter, K., Yan, Y., Delorey, T., Phillips, D. R. & Shah, N. & 14 others, Chaudhary, O., Tsankov, A., Hollmann, T., Rekhtman, N., Massion, P. P., Poirier, J. T., Mazutis, L., Li, R., Lee, J. H., Amon, A., Rudin, C. M., Jacks, T., Regev, A. & Tammela, T., 10 Aug 2020, In: Cancer Cell. 38, 2, p. 229-246.e13

Research output: Contribution to journal › Article › peer-review

Open Access

221 Scopus citations

Regenerative potential of prostate luminal cells revealed by single-cell analysis

Karthaus, W. R., Hofree, M., Choi, D., Linton, E. L., Turkekul, M., Bejnood, A., Carver, B., Gopalan, A., Abida, W., Laudone, V., Biton, M., Chaudhary, O., Xu, T., Masilionis, I., Manova, K., Mazutis, L., Pe’er, D., Regev, A. & Sawyers, C. L., 1 May 2020, In: Science. 368, 6490, p. 497-505 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

174 Scopus citations

2019

A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia

Baryawno, N., Przybylski, D., Kowalczyk, M. S., Kfoury, Y., Severe, N., Gustafsson, K., Kokkaliaris, K. D., Mercier, F., Tabaka, M., Hofree, M., Dionne, D., Papazian, A., Lee, D., Ashenberg, O., Subramanian, A., Vaishnav, E. D., Rozenblatt-Rosen, O., Regev, A. & Scadden, D. T., 13 Jun 2019, In: Cell. 177, 7, p. 1915-1932.e16

Research output: Contribution to journal › Article › peer-review

Open Access

597 Scopus citations

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

Smillie, C. S., Biton, M., Ordovas-Montanes, J., Sullivan, K. M., Burgin, G., Graham, D. B., Herbst, R. H., Rogel, N., Slyper, M., Waldman, J., Sud, M., Andrews, E., Velonias, G., Haber, A. L., Jagadeesh, K., Vickovic, S., Yao, J., Stevens, C., Dionne, D. & Nguyen, L. T. & 13 others, Villani, A. C., Hofree, M., Creasey, E. A., Huang, H., Rozenblatt-Rosen, O., Garber, J. J., Khalili, H., Desch, A. N., Daly, M. J., Ananthakrishnan, A. N., Shalek, A. K., Xavier, R. J. & Regev, A., 25 Jul 2019, In: Cell. 178, 3, p. 714-730.e22

Research output: Contribution to journal › Article › peer-review

Open Access

769 Scopus citations

Intrinsic resistance to immune checkpoint blockade in a mismatch repair–deficient colorectal cancer

Gurjao, C., Liu, D., Hofree, M., AlDubayan, S. H., Wakiro, I., Su, M. J., Felt, K., Gjini, E., Brais, L. K., Rotem, A., Rosenthal, M. H., Rozenblatt-Rosen, O., Rodig, S., Ng, K., Van Allen, E. M., Corsello, S. M., Ogino, S., Regev, A., Nowak, J. A. & Giannakis, M., 2019, In: Cancer Immunology Research. 7, 8, p. 1230-1236 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

63 Scopus citations

Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers

Chatterjee, N., Pazarentzos, E., Mayekar, M. K., Gui, P., Allegakoen, D. V., Hrustanovic, G., Olivas, V., Lin, L., Verschueren, E., Johnson, J. R., Hofree, M., Yan, J. J., Newton, B. W., Dollen, J. V., Earnshaw, C. H., Flanagan, J., Chan, E., Asthana, S., Ideker, T. & Wu, W. & 9 others, Suzuki, J., Barad, B. A., Kirichok, Y., Fraser, J. S., Weiss, W. A., Krogan, N. J., Tulpule, A., Sabnis, A. J. & Bivona, T. G., 27 Aug 2019, In: Cell Reports. 28, 9, p. 2317-2330.e8

Research output: Contribution to journal › Article › peer-review

Open Access

11 Scopus citations

2018

Rapid CLIP dissociation from MHC II promotes an unusual antigen presentation pathway in autoimmunity

Ito, Y., Ashenberg, O., Pyrdol, J., Luoma, A. M., Rozenblatt-Rosen, O., Hofree, M., Christian, E., De Andrade, L. F., Tay, R. E., Teyton, L., Regev, A., Dougan, S. K. & Wucherpfennig, K. W., 1 Oct 2018, In: Journal of Experimental Medicine. 215, 10, p. 2617-2635 19 p.

Research output: Contribution to journal › Article › peer-review

Open Access

22 Scopus citations

2017

Anatomically and Functionally Distinct Lung Mesenchymal Populations Marked by Lgr5 and Lgr6

Lee, J. H., Tammela, T., Hofree, M., Choi, J., Marjanovic, N. D., Han, S., Canner, D., Wu, K., Paschini, M., Bhang, D. H., Jacks, T., Regev, A. & Kim, C. F., 7 Sep 2017, In: Cell. 170, 6, p. 1149-1163.e12

Research output: Contribution to journal › Article › peer-review

Open Access

288 Scopus citations

Exome sequencing of African-American prostate cancer reveals loss-of-function ERF mutations

Huang, F. W., Mosquera, J. M., Garofalo, A., Oh, C., Baco, M., Amin-Mansour, A., Rabasha, B., Bahl, S., Mullane, S. A., Robinson, B. D., Aldubayan, S., Khani, F., Karir, B., Kim, E., Chimene-Weiss, J., Hofree, M., Romanel, A., Osborne, J. R., Kim, J. W. & Azabdaftari, G. & 11 others, Woloszynska-Read, A., Sfanos, K., De Marzo, A. M., Demichelis, F., Gabriel, S., Van Allen, E. M., Mesirov, J., Tamayo, P., Rubin, M. A., Powell, I. J. & Garraway, L. A., Sep 2017, In: Cancer Discovery. 7, 9, p. 973-983 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

98 Scopus citations

Inactivation of Capicua drives cancer metastasis

Okimoto, R. A., Breitenbuecher, F., Olivas, V. R., Wu, W., Gini, B., Hofree, M., Asthana, S., Hrustanovic, G., Flanagan, J., Tulpule, A., Blakely, C. M., Haringsma, H. J., Simmons, A. D., Gowen, K., Suh, J., Miller, V. A., Ali, S., Schuler, M. & Bivona, T. G., 1 Jan 2017, In: Nature Genetics. 49, 1, p. 87-96 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

120 Scopus citations

Interaction landscape of inherited polymorphisms with somatic events in cancer

Carter, H., Marty, R., Hofree, M., Gross, A. M., Jensen, J., Fisch, K. M., Wu, X., Deboever, C., Van Nostrand, E. L., Song, Y., Wheeler, E., Kreisberg, J. F., Lippman, S. M., Yeo, G. W., Gutkind, J. S. & Ideker, T., Apr 2017, In: Cancer Discovery. 7, 4, p. 410-423 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

113 Scopus citations

Massively parallel single-nucleus RNA-seq with DroNc-seq

Habib, N., Avraham-Davidi, I., Basu, A., Burks, T., Shekhar, K., Hofree, M., Choudhury, S. R., Aguet, F., Gelfand, E., Ardlie, K., Weitz, D. A., Rozenblatt-Rosen, O., Zhang, F. & Regev, A., 1 Oct 2017, In: Nature Methods. 14, 10, p. 955-958 4 p.

Research output: Contribution to journal › Article › peer-review

Open Access

688 Scopus citations

The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation

Wallrapp, A., Riesenfeld, S. J., Burkett, P. R., Abdulnour, R. E. E., Nyman, J., Dionne, D., Hofree, M., Cuoco, M. S., Rodman, C., Farouq, D., Haas, B. J., Tickle, T. L., Trombetta, J. J., Baral, P., Klose, C. S. N., Mahlakõiv, T., Artis, D., Rozenblatt-Rosen, O., Chiu, I. M. & Levy, B. D. & 3 others, Kowalczyk, M. S., Regev, A. & Kuchroo, V. K., 21 Sep 2017, In: Nature. 549, 7672, p. 351-356 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

496 Scopus citations

2016

Challenges in identifying cancer genes by analysis of exome sequencing data

Hofree, M., Carter, H., Kreisberg, J. F., Bandyopadhyay, S., Mischel, P. S., Friend, S. & Ideker, T., 15 Jul 2016, In: Nature Communications. 7, 12096.

Research output: Contribution to journal › Article › peer-review

Open Access

31 Scopus citations

Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain

Jaeger, P. A., Lucin, K. M., Britschgi, M., Vardarajan, B., Huang, R. P., Kirby, E. D., Abbey, R., Boeve, B. F., Boxer, A. L., Farrer, L. A., Finch, N., Graff-Radford, N. R., Head, E., Hofree, M., Huang, R., Johns, H., Karydas, A., Knopman, D. S., Loboda, A. & Masliah, E. & 10 others, Narasimhan, R., Petersen, R. C., Podtelezhnikov, A., Pradhan, S., Rademakers, R., Sun, C. H., Younkin, S. G., Miller, B. L., Ideker, T. & Wyss-Coray, T., 26 Apr 2016, In: Molecular Neurodegeneration. 11, 1, 31.

Research output: Contribution to journal › Article › peer-review

Open Access

26 Scopus citations

2015

Functional genome-wide siRNA screen identifies KIAA0586 as mutated in Joubert syndrome

Roosing, S., Hofree, M., Kim, S., Scott, E., Copeland, B., Romani, M., Silhavy, J. L., Rosti, R. O., Schroth, J., Mazza, T., Miccinilli, E., Zaki, M. S., Swoboda, K. J., Milisa-Drautz, J., Dobyns, W. B., Mikati, M., İncecik, F., Azam, M., Borgatti, R. & Romaniello, R. & 24 others, Boustany, R. M., Clericuzio, C. L., D’Arrigo, S., Strømme, P., Boltshauser, E., Stanzial, F., Mirabelli-Badenier, M., Moroni, I., Bertini, E., Emma, F., Steinlin, M., Hildebrandt, F., Johnson, C. A., Freilinger, M., Vaux, K. K., Gabriel, S. B., Aza-Blac, P., Heynen, S. G., Ideker, T., Dynlacht, B. D., Lee, J. E., Valente, E. M., Kim, J. & Gleeson, J. G., 30 May 2015, In: eLife. 4, MAY, p. 1-37 37 p., e06602.

Research output: Contribution to journal › Article › peer-review

Open Access

62 Scopus citations

Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues

Yan, J. F., Kim, H., Jeong, S. K., Lee, H. J., Sethi, M. K., Lee, L. Y., Beavis, R. C., Im, H., Snyder, M. P., Hofree, M., Ideker, T., Wu, S. L., Paik, Y. K., Fanayan, S. & Hancock, W. S., 4 Dec 2015, In: Journal of Proteome Research. 14, 12, p. 4995-5006 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

7 Scopus citations

2014

Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders

Novarino, G., Fenstermaker, A. G., Zaki, M. S., Hofree, M., Silhavy, J. L., Heiberg, A. D., Abdellateef, M., Rosti, B., Scott, E., Mansour, L., Masri, A., Kayserili, H., Al-Aama, J. Y., Abdel-Salam, G. M. H., Karminejad, A., Kara, M., Kara, B., Bozorgmehri, B., Ben-Omran, T. & Mojahedi, F. & 32 others, Mahmoud, I. G. E. D., Bouslam, N., Bouhouche, A., Benomar, A., Hanein, S., Raymond, L., Forlani, S., Mascaro, M., Selim, L., Shehata, N., Al-Allawi, N., Bindu, P. S., Azam, M., Gunel, M., Caglayan, A., Bilguvar, K., Tolun, A., Issa, M. Y., Schroth, J., Spencer, E. G., Rosti, R. O., Akizu, N., Vaux, K. K., Johansen, A., Koh, A. A., Megahed, H., Durr, A., Brice, A., Stevanin, G., Gabriel, S. B., Ideker, T. & Gleeson, J. G., 2014, In: Science. 343, 6170, p. 506-511 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

439 Scopus citations

Integrated Genomic Characterization of Papillary Thyroid Carcinoma

Agrawal, N., Akbani, R., Aksoy, B. A., Ally, A., Arachchi, H., Asa, S. L., Auman, J. T., Balasundaram, M., Balu, S., Baylin, S. B., Behera, M., Bernard, B., Beroukhim, R., Bishop, J. A., Black, A. D., Bodenheimer, T., Boice, L., Bootwalla, M. S., Bowen, J. & Bowlby, R. & 223 others, Bristow, C. A., Brookens, R., Brooks, D., Bryant, R., Buda, E., Butterfield, Y. S. N., Carling, T., Carlsen, R., Carter, S. L., Carty, S. E., Chan, T. A., Chen, A. Y., Cherniack, A. D., Cheung, D., Chin, L., Cho, J., Chu, A., Chuah, E., Cibulskis, K., Ciriello, G., Clarke, A., Clayman, G. L., Cope, L., Copland, J. A., Covington, K., Danilova, L., Davidsen, T., Demchok, J. A., DiCara, D., Dhalla, N., Dhir, R., Dookran, S. S., Dresdner, G., Eldridge, J., Eley, G., El-Naggar, A. K., Eng, S., Fagin, J. A., Fennell, T., Ferris, R. L., Fisher, S., Frazer, S., Frick, J., Gabriel, S. B., Ganly, I., Gao, J., Garraway, L. A., Gastier-Foster, J. M., Getz, G., Gehlenborg, N., Ghossein, R., Gibbs, R. A., Giordano, T. J., Gomez-Hernandez, K., Grimsby, J., Gross, B., Guin, R., Hadjipanayis, A., Harper, H. A., Hayes, D. N., Heiman, D. I., Herman, J. G., Hoadley, K. A., Hofree, M., Holt, R. A., Hoyle, A. P., Huang, F. W., Huang, M., Hutter, C. M., Ideker, T., Iype, L., Jacobsen, A., Jefferys, S. R., Jones, C. D., Jones, S. J. M., Kasaian, K., Kebebew, E., Khuri, F. R., Kim, J., Kramer, R., Kreisberg, R., Kucherlapati, R., Kwiatkowski, D. J., Ladanyi, M., Lai, P. H., Laird, P. W., Lander, E., Lawrence, M. S., Lee, D., Lee, E., Lee, S., Lee, W., Leraas, K. M., Lichtenberg, T. M., Lichtenstein, L., Lin, P., Ling, S., Liu, J., Liu, W., Liu, Y., LiVolsi, V. A., Lu, Y., Ma, Y., Mahadeshwar, H. S., Marra, M. A., Mayo, M., McFadden, D. G., Meng, S., Meyerson, M., Mieczkowski, P. A., Miller, M., Mills, G., Moore, R. A., Mose, L. E., Mungall, A. J., Murray, B. A., Nikiforov, Y. E., Noble, M. S., Ojesina, A. I., Owonikoko, T. K., Ozenberger, B. A., Pantazi, A., Parfenov, M., Park, P. J., Parker, J. S., Paull, E. O., Pedamallu, C. S., Perou, C. M., Prins, J. F., Protopopov, A., Ramalingam, S. S., Ramirez, N. C., Ramirez, R., Raphael, B. J., Rathmell, W. K., Ren, X., Reynolds, S. M., Rheinbay, E., Ringel, M. D., Rivera, M., Roach, J., Robertson, A. G., Rosenberg, M. W., Rosenthal, M., Sadeghi, S., Saksena, G., Sander, C., Santoso, N., Schein, J. E., Schultz, N., Schumacher, S. E., Seethala, R. R., Seidman, J., Senbabaoglu, Y., Seth, S., Sharpe, S., Shaw, K. R. M., Shen, J. P., Shen, R., Sherman, S., Sheth, M., Shi, Y., Shmulevich, I., Sica, G. L., Simons, J. V., Sinha, R., Sipahimalani, P., Smallridge, R. C., Sofia, H. J., Soloway, M. G., Song, X., Sougnez, C., Stewart, C., Stojanov, P., Stuart, J. M., Sumer, S. O., Sun, Y., Tabak, B., Tam, A., Tan, D., Tang, J., Tarnuzzer, R., Taylor, B. S., Thiessen, N., Thorne, L., Thorsson, V., Tuttle, R. M., Umbricht, C. B., Van Den Berg, D. J., Vandin, F., Veluvolu, U., Verhaak, R. G. W., Vinco, M., Voet, D., Walter, V., Wang, Z., Waring, S., Weinberger, P. M., Weinhold, N., Weinstein, J. N., Weisenberger, D. J., Wheeler, D., Wilkerson, M. D., Wilson, J., Williams, M., Winer, D. A., Wise, L., Wu, J., Xi, L., Xu, A. W., Yang, L., Yang, L., Zack, T. I., Zeiger, M. A., Zeng, D., Zenklusen, J. C., Zhao, N., Zhang, H., Zhang, J., Zhang, J., Zhang, W., Zmuda, E. & Zou, L., 23 Oct 2014, In: Cell. 159, 3, p. 676-690 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2422 Scopus citations

Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss

Gross, A. M., Orosco, R. K., Shen, J. P., Egloff, A. M., Carter, H., Hofree, M., Choueiri, M., Coffey, C. S., Lippman, S. M., Hayes, D. N., Cohen, E. E., Grandis, J. R., Nguyen, Q. T. & Ideker, T., 2014, In: Nature Genetics. 46, 9, p. 939-943 5 p.

Research output: Contribution to journal › Article › peer-review

Open Access

106 Scopus citations

2013

Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer

Zhang, E. Y., Cristofanilli, M., Robertson, F., Reuben, J. M., Mu, Z., Beavis, R. C., Im, H., Snyder, M., Hofree, M., Ideker, T., Omenn, G. S., Fanayan, S., Jeong, S. K., Paik, Y. K., Zhang, A. F., Wu, S. L. & Hancock, W. S., 7 Jun 2013, In: Journal of Proteome Research. 12, 6, p. 2805-2817 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

40 Scopus citations

Network-based stratification of tumor mutations

Hofree, M., Shen, J. P., Carter, H., Gross, A. & Ideker, T., Nov 2013, In: Nature Methods. 10, 11, p. 1108-1118 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

607 Scopus citations

Using functional signature ontology (FUSION) to identify mechanisms of action for Natural products

Potts, M. B., Kim, H. S., Fisher, K. W., Hu, Y., Carrasco, Y. P., Bulut, G. B., Ou, Y. H., Herrera-Herrera, M. L., Cubillos, F., Mendiratta, S., Xiao, G., Hofree, M., Ideker, T., Xie, Y., Huang, L. J. S., Lewis, R. E., MacMillan, J. B. & White, M. A., 15 Oct 2013, In: Science Signaling. 6, 297, ra90.

Research output: Contribution to journal › Article › peer-review

Open Access

61 Scopus citations

2011

RepTar: A database of predicted cellular targets of host and viral miRNAs

Elefant, N., Berger, A., Shein, H., Hofree, M., Margalit, H. & Altuvia, Y., Jan 2011, In: Nucleic Acids Research. 39, SUPPL. 1, p. D188-D194

Research output: Contribution to journal › Article › peer-review

Open Access

45 Scopus citations

Matan Hofree

Research output

Search results