|Integrated Genomic Characterization of Papillary Thyroid Carcinoma|
Cell 159 (3), 679-690, 2014
|Network-based stratification of tumor mutations|
M Hofree, JP Shen, H Carter, A Gross, T Ideker
Nature methods 10 (11), 1108-1115, 2013
|Massively parallel single-nucleus RNA-seq with DroNc-seq|
N Habib, I Avraham-Davidi, A Basu, T Burks, K Shekhar, M Hofree, ...
Nature methods 14 (10), 955-958, 2017
|Intra-and inter-cellular rewiring of the human colon during ulcerative colitis|
CS Smillie, M Biton, J Ordovas-Montanes, KM Sullivan, G Burgin, ...
Cell 178 (3), 714-730. e22, 2019
|Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders|
G Novarino, AG Fenstermaker, MS Zaki, M Hofree, JL Silhavy, ...
science 343 (6170), 506-511, 2014
|The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation|
A Wallrapp, SJ Riesenfeld, PR Burkett, REE Abdulnour, J Nyman, ...
Nature 549 (7672), 351-356, 2017
|A cellular taxonomy of the bone marrow stroma in homeostasis and leukemia|
N Baryawno, D Przybylski, MS Kowalczyk, Y Kfoury, N Severe, ...
Cell 177 (7), 1915-1932. e16, 2019
|A decade of systems biology|
HY Chuang, M Hofree, T Ideker
Annual review of cell and developmental biology 26, 721-744, 2010
|Anatomically and functionally distinct lung mesenchymal populations marked by Lgr5 and Lgr6|
JH Lee, T Tammela, M Hofree, J Choi, ND Marjanovic, S Han, D Canner, ...
Cell 170 (6), 1149-1163. e12, 2017
|A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors|
M Slyper, CBM Porter, O Ashenberg, J Waldman, E Drokhlyansky, ...
Nature medicine 26 (5), 792-802, 2020
|Emergence of a high-plasticity cell state during lung cancer evolution|
ND Marjanovic, M Hofree, JE Chan, D Canner, K Wu, M Trakala, ...
Cancer cell 38 (2), 229-246. e13, 2020
|Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss|
AM Gross, RK Orosco, JP Shen, AM Egloff, H Carter, M Hofree, ...
Nature genetics 46 (9), 939-943, 2014
|Genotype to phenotype via network analysis|
H Carter, M Hofree, T Ideker
Current opinion in genetics & development 23 (6), 611-621, 2013
|Inactivation of Capicua drives cancer metastasis|
RA Okimoto, F Breitenbuecher, VR Olivas, W Wu, B Gini, M Hofree, ...
Nature genetics 49 (1), 87-96, 2017
|Regenerative potential of prostate luminal cells revealed by single-cell analysis|
WR Karthaus, M Hofree, D Choi, EL Linton, M Turkekul, A Bejnood, ...
Science 368 (6490), 497-505, 2020
|Interaction landscape of inherited polymorphisms with somatic events in cancer|
H Carter, R Marty, M Hofree, AM Gross, J Jensen, KM Fisch, X Wu, ...
Cancer discovery 7 (4), 410-423, 2017
|Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF MutationsExome Sequencing of African-American Prostate Cancer|
FW Huang, JM Mosquera, A Garofalo, C Oh, M Baco, A Amin-Mansour, ...
Cancer discovery 7 (9), 973-983, 2017
|Spatially organized multicellular immune hubs in human colorectal cancer|
K Pelka, M Hofree, JH Chen, S Sarkizova, JD Pirl, V Jorgji, A Bejnood, ...
Cell 184 (18), 4734-4752. e20, 2021
|Using functional signature ontology (FUSION) to identify mechanisms of action for natural products|
MB Potts, HS Kim, KW Fisher, Y Hu, YP Carrasco, GB Bulut, YH Ou, ...
Science signaling 6 (297), ra90-ra90, 2013
|Functional genome-wide siRNA screen identifies KIAA0586 as mutated in Joubert syndrome|
S Roosing, M Hofree, S Kim, E Scott, B Copeland, M Romani, JL Silhavy, ...
Elife 4, e06602, 2015