Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing
Tsion Abay, Robert R. Stickels, Meril T. Takizawa, Benan N. Nalbant, Yu-Hsin Hsieh, Sidney Hwang, Catherine Snopkowski, Kenny Kwok Hei Yu, Zaki Abou-Mrad, Viviane Tabar, Brooke E. Howitt, Leif S. Ludwig, Ronan Chaligné, Ansuman T. Satpathy & Caleb A. Lareau
Nature Genetics, 8 January 2025
Multi-modal analysis reveals tumor and immune features distinguishing EBV-positive and EBV-negative post-transplant lymphoproliferative disorders
Jiaying Toh, Andrea J Reitsma, Tetsuya Tajima, Sheren F Younes, Chimere Ezeiruaku, Kayla C Jenkins, Josselyn K Peña, Shuchun Zhao, Xi Wang, Esmond Y Z Lee, Marla C Glass, Laurynas Kalesinskas, Ananthakrishnan Ganesan, Irene Liang, Joy A Pai, James T Harden, Francesco Vallania, Edward A Vizcarra, Govind Bhagat, Fiona E Craig, Steven H Swerdlow, Julie Morscio, Daan Dierickx, Thomas Tousseyn, Ansuman T Satpathy, Sheri M Krams, Yasodha Natkunam, Purvesh Khatri, Olivia M Martinez
Cell Reports Medicine, 17 December 2024
Central control of dynamic gene circuits governs T cell rest and activation
Maya M Arce, Jennifer M Umhoefer, Nadia Arang, Sivakanthan Kasinathan, Jacob W Freimer, Zachary Steinhart, Haolin Shen, Minh T N Pham, Mineto Ota, Anika Wadhera, Rama Dajani, Dmytro Dorovskyi, Yan Yi Chen, Qi Liu, Yuan Zhou, Danielle L Swaney, Kirsten Obernier, Brian R Shy, Julia Carnevale, Ansuman T Satpathy, Nevan J Krogan, Jonathan K Pritchard, Alexander Marson
Nature, 11 December 2024
Temporal genomic analysis of homogeneous tumor models reveals key regulators of immune evasion in melanoma
Sapir Cohen Shvefel, Joy A Pai, Yingying Cao, Lipika R Pal, Osnat Bartok, Ronen Levy, Marie J Zemanek, Chen Weller, Ella Herzog, Winnie Yao, Kamir J Hiam-Galvez, Kuoyuan Cheng, Yajie Yin, Peter P Du, Colin J Raposo, Nofar Gumpert, Michele Welti, Julia M Martínez Gómez, Federica Sella, Elizabeta Yakubovich, Irit Orr, Shifra Ben-Dor, Roni Oren, Liat Fellus-Alyagor, Ofra Golani, Ori Jacob Brenner, Tomer M Salame, Mirie Zerbib, Inna Goliand, Dean Ranmar, Ilya Savchenko, Nadav Ketrarou, Alejandro A Schaffer, Rony Dahan, Mitchell P Levesque, Eytan Ruppin, Ansuman T Satpathy, Yardena Samuels
Cancer Discovery, 20 November 2024
Retinoic acid and TGF-β orchestrate organ-specific programs of tissue residency
Andreas Obers, Tobias Poch, Grace Rodrigues, Susan N Christo, Luke C Gandolfo, Raissa Fonseca, Ali Zaid, Joey En Yu Kuai, Hongjin Lai, Pirooz Zareie, Marina H Yakou, Lachlan Dryburgh, Thomas N Burn, James Dosser, Frank A Buquicchio, Caleb A Lareau, Calum Walsh, Louise Judd, Maria Rafailia Theodorou, Katharina Gutbrod, Peter Dörmann, Jenny Kingham, Tim Stinear, Axel Kallies, Jan Schroeder, Scott N Mueller, Simone L Park, Terence P Speed, Ansuman T Satpathy, Tri Giang Phan, Christoph Wilhelm, Colby Zaph, Maximilien Evrard, Laura K Mackay
Immunity, 12 November 2024
Deciphering the impact of genomic variation on function
IGVF Consortium
Nature, 4 September 2024
Distinct epigenomic landscapes underlie tissue-specific memory T cell differentiation
Frank A Buquicchio, Raissa Fonseca, Patrick K Yan, Fangyi Wang, Maximilien Evrard, Andreas Obers, Jacob C Gutierrez, Colin J Raposo, Julia A Belk, Bence Daniel, Pirooz Zareie, Kathryn E Yost, Yanyan Qi, Yajie Yin, Katherine F Nico, Flora M Tierney, Michael R Howitt, Caleb A Lareau, Ansuman T Satpathy, Laura K Mackay
Immunity, 16 July 2024
The temporal progression of lung immune remodeling during breast cancer metastasis
Christopher S McGinnis, Zhuang Miao, Daphne Superville, Winnie Yao, Andrei Goga, Nathan E Reticker-Flynn, Juliane Winkler, Ansuman T Satpathy
Cancer Cell, 10 June 2024
Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells
Cody T Mowery, Jacob W Freimer, Zeyu Chen, Salvador Casaní-Galdón, Jennifer M Umhoefer, Maya M Arce, Ketrin Gjoni, Bence Daniel, Katalin Sandor, Benjamin G Gowen, Vinh Nguyen, Dimitre R Simeonov, Christian M Garrido, Gemma L Curie, Ralf Schmidt, Zachary Steinhart, Ansuman T Satpathy, Katherine S Pollard, Jacob E Corn, Bradley E Bernstein, Chun Jimmie Ye, Alexander Marson
Nature Genetics, 29 May 2024
Direct transposition of native DNA for sensitive multimodal single-molecule sequencing
Arjun S Nanda, Ke Wu, Iryna Irkliyenko, Brian Woo, Megan S Ostrowski, Andrew S Clugston, Leanne C Sayles, Lingru Xu, Ansuman T Satpathy, Hao G Nguyen, E Alejandro Sweet-Cordero, Hani Goodarzi, Sivakanthan Kasinathan, Vijay Ramani
Nature Genetics, 9 May 2024