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SlideCNA: spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data Zhang, Diane; Segerstolpe, Asa; Slyper, Michal; Waldman, Julia; Murray, Evan; Strasser, Robert; Watter, Jan; Cohen, Ofir; Ashenberg, Orr; Abravanel, Daniel; Jane-Valbuena, Judit; Mages, Simon; Lako, Ana; Helvie, Karla; Rozenblatt-Rosen, Orit; Rodig, Scott; Chen, Fei; Wagle, Nikhil; Regev, Aviv; Klughammer, Johanna Share Save
A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features Klughammer, Johanna; Abravanel, Daniel L.; Segerstolpe, Asa; Blosser, Timothy R.; Goltsev, Yury; Cui, Yi; Goodwin, Daniel R.; Sinha, Anubhav; Ashenberg, Orr; Slyper, Michal; Vigneau, Sebastien; Jane-Valbuena, Judit; Alon, Shahar; Caraccio, Chiara; Chen, Judy; Cohen, Ofir; Cullen, Nicole; DelloStritto, Laura K.; Dionne, Danielle; Files, Janet; Frangieh, Allison; Helvie, Karla; Hughes, Melissa E.; Inga, Stephanie; Kanodia, Abhay; Lako, Ana; MacKichan, Colin; Mages, Simon; Moriel, Noa; Murray, Evan; Napolitano, Sara; Nguyen, Kyleen; Nitzan, Mor; Ortiz, Rebecca; Patel, Miraj; Pfaff, Kathleen L.; Porter, Caroline B. M.; Rotem, Asaf; Strauss, Sarah; Strasser, Robert; Thorner, Aaron R.; Turner, Madison; Wakiro, Isaac; Waldman, Julia; Wu, Jingyi; Zanudo, Jorge Gomez Tejeda; Zhang, Diane; Lin, Nancy U.; Tolaney, Sara M.; Winer, Eric P.; Boyden, Edward S.; Chen, Fei; Nolan, Garry P.; Rodig, Scott J.; Zhuang, Xiaowei; Rozenblatt-Rosen, Orit; Johnson, Bruce E.; Regev, Aviv; Wagle, Nikhil Share Save
Characterization and proposed therapeutic exploitation of fusion RNAs in metastatic breast cancers Priedigkeit, Nolan; Lebron-Torres, Alines; Liao, Janny; Alberge, Jean-Baptiste; Morganti, Stefania; Weiss, Jakob; Zanudo, Jorge Gomez Tejeda; Grinshpun, Albert; Hughes, Melissa; Helvie, Karla; Sendrick, Kerry; Nguyen, Kyleen; Strauss, Sarah; Files, Janet; Lloyd, Maxwell; Wagle, Nikhil; Stewart, Chip; Winer, Eric; Johnson, Bruce; Li, Yvonne; Jeselsohn, Rinath; Tolaney, Sara; Abravanel, Daniel; Lin, Nancy; Parsons, Heather; Getz, Gad; Oesterreich, Steffi; Lee, Adrian; Golub, Todd Share Save
Exemestane plus everolimus and palbociclib in metastatic breast cancer: clinical response and genomic/transcriptomic determinants of resistance in a phase I/II trial Zanudo, Jorge Gomez Tejeda; Barroso-Sousa, Romualdo; Jain, Esha; Jin, Qingchun; Li, Tianyu; Buendia-Buendia, Jorge E.; Pereslete, Alyssa; Abravanel, Daniel L.; Ferreira, Arlindo R.; Wrabel, Eileen; Helvie, Karla; Hughes, Melissa E.; Partridge, Ann H.; Overmoyer, Beth; Lin, Nancy U.; Tayob, Nabihah; Tolaney, Sara M.; Wagle, Nikhil Share Save
Genomic and transcriptomic analysis reveals known and novel resistance mechanisms to CDK4/6 inhibitors and sensitivity factors for the response to triplet therapy (palbociclib plus everolimus plus exemestane) in a phase I/IIb study in hormone-receptor positive (HR+)/HER2-metastatic breast cancer (MBC) after progression on a CDK4/6 inhibitor (CDK4/6i) Zanudo, Jorge Gomez Tejeda; Barroso-Sousa, Romualdo; Jain, Esha; Buendia-Buendia, Jorge; Li, Tianyu; Tayob, Nabihah; Rees, Rebecca; Pereslete, Alyssa; Ferreira, Arlindo R.; Abravanel, Daniel L.; Helvie, Karla; Partridge, Ann H.; Overmoyer, Beth; Winer, Eric P.; Wagle, Nikhil; Tolaney, Sara M. Share Save
The metastatic breast cancer project - Expanding the clinical, genomic, and transcriptomic landscape of metastatic breast cancer through patient-partnered research Jain, Esha; Kim, Dewey; Zanudo, Jorge Gomez Tejeda; Balch, Sara; McGillicuddy, Mary; Tomson, Brett N.; Hernandez, Tania G.; Thomas, Beena S.; Abravanel, Daniel L.; Shah, Shahrayz; Ramos, Rafael; Sosa, Delia; Small, Ilan; Sterlin, Lauren; Winnicki, Sarah; Nguyen, Colleen; Dunphy, Micheal; Anastasio, Elana; Golub, Todd R.; Painter, Corrie A.; Wagle, Nikhil Share Save
Spatio-molecular dissection of the breast cancer metastatic microenvironment Abravanel, Daniel L.; Klughammer, Johanna; Blosser, Timothy; Goltsev, Yury; Jiang, Sizun; Bai, Yunjao; Murray, Evan; Alon, Shahar; Cui, Yi; Goodwin, Daniel R.; Sinha, Anubhav; Cohen, Ofir; Slyper, Michal; Ashenberg, Orr; Dionne, Danielle; Jane-Valbuena, Judit; Porter, Caroline BM.; Segerstolpe, Asa; Waldman, Julia; Vigneau, Sebastien; Helvie, Karla; Frangieh, Allison; DelloStritto, Laura; Patel, Miraj; We, Jingyi; Pfaff, Kathleen; Cullen, Nicole; Lako, Ana; Turner, Madison; Wakiro, Isaac; Napolitano, Sara; Kanodia, Abhay; Ortiz, Rebecca; MacKichan, Colin; Inga, Stephanie; Chen, Judy; Thorner, Aaron R.; Rotem, Asaf; Rodig, Scott; Chen, Fei; Boyden, Edward S.; Nolan, Garry P.; Zhuang, Xiaowei; Rozenblatt-Rosen, Orit; Johnson, Bruce E.; Regev, Aviv; Wagle, Nikhil Share Save
The metastatic breast cancer project: Generating the clinical and genomic landscape of metastatic breast cancer through patient-partnered research Wagle, Nikhil; Painter, Corrie; Anastasio, Elana; McGillicuddy, Mary; Jain, Esha; Hernandez, Tania G.; Tomson, Brett N.; Thomas, Beena; Abravanel, Daniel; Kim, Dewey; Balch, Sara; Damon, Alyssa L.; Shah, Shahrayz; Ramos, Rafael; Sosa, Delia; Small, Ilan; Nguyen, Colleen; Winnicki, Sarah; Cusher, Taylor; Chastain, Parker; Dunphy, Michael; Zanudo, Jorge Gomez Tejeda; Tsegai, Netsanet; Sterlin, Lauren; Ulysse, Ulcha F.; Boykin, Imani; Alao, Oyin; Golub, Todd R. Share Save
Acquired activating mutations in RTKs confer endocrine resistance in ER plus metastatic breast cancer through ER-reprogramming, MAPK signaling, and an induced stem-like cell state Cohen, Ofir; Mao, Pingping; Nayar, Utthara; Buendia-Bue, Jorge E.; Kim, Dewey; Jain, Esha; Helvie, Karla; Abravanel, Daniel; Kowalski, Kailey J.; Kapstad, Christian; Freeman, Samuel; Adalsteinsson, Victor; Wander, Seth A.; Waks, Adrienne G.; Getz, Gad; Regev, Aviv; Winer, Eric P. Winer; Lin, Nancy U. Nancy U.; Wagle, Nikhil Share Save
A joint atlas of single-cell and bulk RNA-seq in metastatic breast cancer allows inference of oncogenic and drug-resistant transcriptional programs in malignant cells and the tumor microenvironment Cohen, Ofir; Abravanel, Daniel; Slyper, Michal; Klughammer, Johanna; Jane-Valbuena, Judit; Helvie, Karla; Dellostritto, Laura; Frangieh, Allison; Vigneau, Sebastien; Wu, Jingyi; Mayorga, Angie; Waldman, Julia; Nguyen, Lan; Dionne, Danielle; Ashenberg, Orr; Hofree, Matan; Cuoco, Mike; Rodman, Christopher; Winer, Eric P.; Lin, Nancy; Johnson, Bruce; Rotem, Asaf; Rozenblatt-Rosen, Orit; Regev, Aviv; Wagle, Nikhil Share Save
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Inhibition of γ-Secretase Activity Inhibits Tumor Progression in a Mouse Model of Pancreatic Ductal Adenocarcinoma Plentz, Ruben; Park, Ji-Sun; Rhim, Andrew D.; Abravanel, Daniel; Hezel, Aram F.; Sharma, Sreenath V.; Gurumurthy, Sushma; Deshpande, Vikram; Kenific, Candia; Settleman, Jeffrey; Majumder, Pradip K.; Stanger, Ben Z.; Bardeesy, Nabeel Share Save
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