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Matan Hofree

 https://orcid.org/0000-0001-8368-0299
    Calculated based on number of publications stored in Pure and citations from Scopus
    20102024

    Research activity per year

    Search results

    • 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
      39 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
      11 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
      29 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
      71 Scopus citations

    • Integrative single cell and spatial transcriptomics of colorectal cancer reveals multicellular functional units that support tumor progression

      Avraham-Davidi, I., Mages, S., Klughammer, J., Moriel, N., Imada, S., Hofree, M., Murray, E., Chen, J., Pelka, K., Mehta, A., Boland, G. M., Delorey, T., Caplan, L., Dionne, D., Tirosh, I., Hacohen, N., Chen, F., Yilmaz, O., Roper, J. & Rozenblatt-Rosen, O. & 2 others, Nitzan, M. & Regev, A., 1 Jan 2022, (bioRxiv).

      Research output: Working paper/preprint › Preprint

      Open Access

    • 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
      12 Scopus citations

    • Multi-modal single-cell and whole-genome sequencing of minute, frozen specimens to propel clinical applications

      Wang, Y., Fan, J. L., Melms, J. C., Amin, A. D., Georgis, Y., Ho, P., Tagore, S., Abril-Rodríguez, G., Biermann, J., Hofree, M., Caprio, L., Berhe, S., Khan, S. A., Henick, B. S., Ribas, A., Taylor, A. M., Schwartz, G. K., Carvajal, R. D., Azizi, E. & Izar, B., 2022, (bioRxiv).

      Research output: Working paper/preprint › Preprint

      Open Access
    • 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
      170 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

    • Metabolic Regulation of SARS-CoV-2 Infection

      Ehrlich, A., Ioannidis, K., Nasar, M., Alkian, I. A., Hofree, M., Tikva, S. S., Rainy, N., Houri, I., Cicero, A., Pavanello, C., Sirtori, C. R., Cohen, J. B., Chirinos, J. A., Deutsch, L., Gottlieb, A., Bar-Chaim, A., Shibolet, O., Maayan, S. L. & Nahmias, Y., 2021, (ResearchSquare).

      Research output: Working paper/preprint › Preprint

    • Multicellular immune hubs and their organization in MMRd and MMRp colorectal cancer

      Pelka, K., Hofree, M., Chen, J., 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. & 51 others, Wakiro, I., Cohen, O., 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., 2021, (bioRxiv).

      Research output: Working paper/preprint › Preprint

      Open Access

    • Parental-fetal interplay of immune genes leads to intrauterine growth restriction

      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., Davidi, I. A., 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., 2021, (bioRxiv).

      Research output: Working paper/preprint › Preprint

      Open Access

    • 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
      385 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
      418 Scopus citations

    • Author Correction: A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors (Nature Medicine, (2020), 26, 5, (792-802), 10.1038/s41591-020-0844-1)

      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 Aug 2020, In: Nature Medicine. 26, 8, p. 1307 1 p.

      Research output: Contribution to journal › Comment/debate

      Open Access
      16 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
      226 Scopus citations

    • Mutant EZH2 Drives Follicular Lymphoma by Altering B-cell Dependencies

      Karthaus, W. R., Hofree, M., Choi, D., Linton, E. L., Turkekul, M. & Bejnood, A., 1 Jul 2020, In: Cancer Discovery. 10, 7, p. 900-900 1 p.

      Research output: Contribution to journal › Comment/debate

      Open Access

    • 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
      177 Scopus citations

    • The SARS-CoV-2 Transcriptional Metabolic Signature in Lung Epithelium

      Ehrlich, A., Uhl, S., Ioannidis, K., Hofree, M., tenOever, B. R. & Nahmias, Y., 2020, (SSRN).

      Research output: Working paper/preprint › Preprint

      Open Access
    • 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
      603 Scopus citations

    • A cellular taxonomy of the bone marrow stroma in homeostasis and leukemia demonstrates cancer-crosstalk with stroma to impair normal tissue function

      Ninib, B., Dariusz, P., Kowalczyk, M. S., Youmna, K., Nicolas, S., Karin, G., Francois, M., Marcin, T., Matan, H., Danielle, D., Ani, P., Dongjun, L., Orit, R.-R., Aviv, R. & Scadden, D. T., 1 Jan 2019, (bioRxiv).

      Research output: Working paper/preprint › Preprint

      Open Access

    • 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
      781 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
      64 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

    • Synthetic essentiality of metabolic regulator PDHK1 in PTEN-deficient cells and cancers

      Chatterjee, N., Pazarentzos, E., Hrustanovic, G., Lin, L., Verschueren, E., Johnson, J. R., Hofree, M., Yan, J. J., Olivas, V., Newton, B. W., Dollen, J. V., Earnshaw, C. H., Flanagan, J., Chan, E., Asthana, S., Ideker, T., Wu, W., Mayekar, M. K., Suzuki, J. & Barad, B. & 7 others, Kirichok, Y., Fraser, J., Weiss, W. A., Krogan, N. J., Tulpule, A., Sabnis, A. J. & Bivona, T. G., 2018, (bioRxiv).

      Research output: Working paper/preprint › Preprint

      Open Access
    • 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
      289 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
      121 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
      114 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
      693 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
      502 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

    • Identifying mutation specific cancer pathways using a structurally resolved protein interaction network

      Engin, H. B., Hofree, M. & Carter, H., 2015, In: Pacific Symposium on Biocomputing. p. 84-95 12 p.

      Research output: Contribution to journal › Conference article › peer-review

      9 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
      442 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
      2444 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

    • Genotype to phenotype via network analysis

      Carter, H., Hofree, M. & Ideker, T., Dec 2013, In: Current Opinion in Genetics and Development. 23, 6, p. 611-621 11 p.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      95 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
      611 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
    • 2010

      A decade of systems biology

      Chuang, H. Y., Hofree, M. & Ideker, T., 10 Nov 2010, In: Annual Review of Cell and Developmental Biology. 26, p. 721-744 24 p.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      264 Scopus citations
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