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 journalArticlepeer-review

    3 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 journalArticlepeer-review

    Open Access
  • 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., Alkian, I. A., Daskal, Y., Atari, N., Kliker, L., Rainy, N., Hofree, M., Tikva, S. 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., Jan 2023, In: eLife. 12, e79946.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    6 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 journalArticlepeer-review

    Open Access
    13 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 journalArticlepeer-review

    Open Access
    50 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/preprintPreprint

    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 journalArticlepeer-review

    Open Access
    7 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/preprintPreprint

    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 journalArticlepeer-review

    Open Access
    117 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 journalArticlepeer-review

    Open Access
    15 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/preprintPreprint

  • 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/preprintPreprint

    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/preprintPreprint

    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 journalArticlepeer-review

    Open Access
    248 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 journalArticlepeer-review

    Open Access
    56 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 journalArticlepeer-review

    Open Access
    313 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 journalComment/debate

    Open Access
    13 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 journalArticlepeer-review

    Open Access
    179 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 journalComment/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 journalArticlepeer-review

    Open Access
    145 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/preprintPreprint

    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 journalArticlepeer-review

    Open Access
    550 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/preprintPreprint

    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 journalArticlepeer-review

    Open Access
    649 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 journalArticlepeer-review

    Open Access
    58 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 journalArticlepeer-review

    Open Access
    9 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 journalArticlepeer-review

    Open Access
    20 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/preprintPreprint

    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 journalArticlepeer-review

    Open Access
    264 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 journalArticlepeer-review

    Open Access
    85 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 journalArticlepeer-review

    Open Access
    115 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 journalArticlepeer-review

    Open Access
    108 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 journalArticlepeer-review

    Open Access
    615 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 journalArticlepeer-review

    Open Access
    433 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 journalArticlepeer-review

    Open Access
    28 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 journalArticlepeer-review

    Open Access
    24 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 journalArticlepeer-review

    Open Access
    59 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 journalConference articlepeer-review

    8 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 journalArticlepeer-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 journalArticlepeer-review

    Open Access
    416 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 journalArticlepeer-review

    Open Access
    2227 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 journalArticlepeer-review

    Open Access
    103 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 journalArticlepeer-review

    Open Access
    36 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 journalReview articlepeer-review

    Open Access
    94 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 journalArticlepeer-review

    Open Access
    584 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 journalArticlepeer-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 journalArticlepeer-review

    Open Access
    44 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 journalReview articlepeer-review

    Open Access
    253 Scopus citations
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