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Neuropath-AI, a histopathology-based deep learning classifier for CNS tumors, achieves and improves human neuropathologist-level performance Lalchungnunga, H.; Dampier, Christopher H.; Singh, Omkar; Hoang, Danh-Tai; Shulman, Eldad D.; Abdullaev, Zied; Li, Bochong; Luo, Zhirui; Pearce, Thomas; Marker, Daniel F.; Horbinski, Craig; Lucas, Calixto-Hope G.; Cimino, Patrick J.; Nasrallah, MacLean P.; Quezado, Martha; Chung, Hye-Jung; Yefet, Leeor; Zadeh, Gelareh; Brandner, Sebastian; Ruppin, Eytan; Aldape, Kenneth Share Save
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Tumor and blood B-cell abundance outperforms established immune checkpoint blockade response prediction signatures in head and neck cancer Chang, T. -g.; Spathis, A.; Schaffer, A. A.; Gavrielatou, N.; Kuo, F.; Jia, D.; Mukherjee, S.; Sievers, C.; Economopoulou, P.; Anastasiou, M.; Moutafi, M.; Pal, L. R.; Vos, J.; Lee, A. S.; Lam, S.; Zhao, K.; Jiang, P.; Allen, C. T.; Foukas, P.; Gomatou, G.; Altan-Bonnet, G.; Morris, L. G. T.; Psyrri, A.; Ruppin, E. Share Save
Charting the transcriptomic landscape of primary and metastatic cancers in relation to their origin and target normal tissues Sanghvi, Neel; Calvo-Alcaniz, Camilo; Rajagopal, Padma S.; Scalera, Stefano; Canu, Valeria; Sinha, Sanju; Schischlik, Fiorella; Wang, Kun; Madan, Sanna; Shulman, Eldad; Papanicolau-Sengos, Antonios; Blandino, Giovanni; Ruppin, Eytan; Nair, Nishanth Ulhas Share Save
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A machine learning model reveals expansive downregulation of ligand-receptor interactions that enhance lymphocyte infiltration in melanoma with developed resistance to immune checkpoint blockade Sahni, Sahil; Wang, Binbin; Wu, Di; Dhruba, Saugato Rahman; Nagy, Matthew; Patkar, Sushant; Ferreira, Ingrid; Day, Chi-Ping; Wang, Kun; Ruppin, Eytan Share Save
Increased RNA and Protein Degradation Is Required for Counteracting Transcriptional Burden and Proteotoxic Stress in Human Aneuploid Cells Ippolito, Marica Rosaria; Zerbib, Johanna; Eliezer, Yonatan; Reuveni, Eli; Vigano, Sonia; De Feudis, Giuseppina; Shulman, Eldad D.; Kadmon, Anouk Savir; Slutsky, Rachel; Chang, Tiangen; Campagnolo, Emma M.; Taglietti, Silvia; Scorzoni, Simone; Gianotti, Sara; Martin, Sara; Muenzner, Julia; Muelleder, Michael; Rozenblum, Nir; Rubolino, Carmela; Ben-Yishay, Tal; Laue, Kathrin; Cohen-Sharir, Yael; Vigorito, Ilaria; Nicassio, Francesco; Ruppin, Eytan; Ralser, Markus; Vazquez, Francisca; Santaguida, Stefano; Ben-David, Uri Share Save
Chromosome 7 Gain Compensates for Chromosome 10 Loss in Glioma Nair, Nishanth Ulhas; Schaffer, Alejandro A.; Gertz, E. Michael; Cheng, Kuoyuan; Zerbib, Johanna; Sahu, Avinash Das; Leor, Gil; Shulman, Eldad D.; Aldape, Kenneth D.; Ben-David, Uri; Ruppin, Eytan Share Save
Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes Robinson, Welles; Stone, Joshua K.; Schischlik, Fiorella; Gasmi, Billel; Kelly, Michael C.; Seibert, Charlie; Dadkhah, Kimia; Gertz, E. Michael; Lee, Joo Sang; Zhu, Kaiyuan; Ma, Lichun; Wang, Xin Wei; Sahinalp, S. Cenk; Patro, Rob; Leiserson, Mark D. M.; Harris, Curtis C.; Schaffer, Alejandro A.; Ruppin, Eytan Share Save
ASS1 metabolically contributes to the nuclear and cytosolic p53-mediated DNA damage response (04 July, 10.1038/s42255-024-01090-z) Lim, Lisha Qiu Jin; Adler, Lital; Hajaj, Emma; Soria, Leandro R.; Perry, Rotem Ben-Tov; Darzi, Naama; Brody, Ruchama; Furth, Noa; Lichtenstein, Michal; Bab-Dinitz, Elizabeta; Porat, Ziv; Melman, Tevie; Brandis, Alexander; Malitsky, Sergey; Itkin, Maxim; Aylon, Yael; Ben-Dor, Shifra; Orr, Irit; Pri-Or, Amir; Seger, Rony; Shaul, Yoav; Ruppin, Eytan; Oren, Moshe; Perez, Minervo; Meier, Jordan; Brunetti-Pierri, Nicola; Shema, Efrat; Ulitsky, Igor; Erez, Ayelet Share Save
A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics Hoang, Danh-Tai; Dinstag, Gal; Shulman, Eldad D.; Hermida, Leandro C.; Ben-Zvi, Doreen S.; Elis, Efrat; Caley, Katherine; Sammut, Stephen-John; Sinha, Sanju; Sinha, Neelam; Dampier, Christopher H.; Stossel, Chani; Patil, Tejas; Rajan, Arun; Lassoued, Wiem; Strauss, Julius; Bailey, Shania; Allen, Clint; Redman, Jason; Beker, Tuvik; Jiang, Peng; Golan, Talia; Wilkinson, Scott; Sowalsky, Adam G.; Pine, Sharon R.; Caldas, Carlos; Gulley, James L.; Aldape, Kenneth; Aharonov, Ranit; Stone, Eric A.; Ruppin, Eytan Share Save
ASS1 metabolically contributes to the nuclear and cytosolic p53-mediated DNA damage response Lim, Lisha Qiu Jin; Adler, Lital; Hajaj, Emma; Soria, Leandro R.; Perry, Rotem Ben-Tov; Darzi, Naama; Brody, Ruchama; Furth, Noa; Lichtenstein, Michal; Bab-Dinitz, Elizabeta; Porat, Ziv; Melman, Tevie; Brandis, Alexander; Aylon, Yael; Ben-Dor, Shifra; Orr, Irit; Pri-Or, Amir; Seger, Rony; Shaul, Yoav; Ruppin, Eytan; Oren, Moshe; Perez, Minervo; Meier, Jordan; Brunetti-Pierri, Nicola; Shema, Efrat; Ulitsky, Igor; Erez, Ayelet; Malitsky, Sergey; Itkin, Maxim Share Save
LORIS robustly predicts patient outcomes with immune checkpoint blockade therapy using common clinical, pathologic and genomic features Chang, Tian-Gen; Cao, Yingying; Sfreddo, Hannah J.; Dhruba, Saugato Rahman; Lee, Se-Hoon; Valero, Cristina; Yoo, Seong-Keun; Chowell, Diego; Morris, Luc G. T.; Ruppin, Eytan Share Save
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