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Jeffrey R. Moffitt

Boston Children's Hospital

39H-index
116Paper Count
1.4WCitation Count
Published Papers 35
Publication Date
An image-based transcriptomics atlas reveals the regional and microbiota-dependent molecular, cellular, and spatial structure of the murine gut
err2026-02-19
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errRosalind J. Xu; Hao Zhang; Paolo Cadinu; Phillip B. Nicol; Uli S. Herrmann; Tyrone Lee; Ludwig Geistlinger; Rafael A. Irizarry; Jeffrey R. Moffitt
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A spatial atlas of the complement system uncovers unique expression patterns in postnatal brain development in mice
err2025-12-02
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errOAAI
errYingying Zhang; Brianna Watson; Ajitanuj Rattan; Tyrone Lee; Smriti Chawla; Ludwig Geistlinger; Yilin Guan; Finley B. Lord; Minghe Ma; Takashi Miwa; Madhu Golla; Barbara J. Caldarone; Wen-chao Song; Jeffrey R. Moffitt; Michael C. Carroll
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Author Correction: Spatial transcriptomics reveals the distinct organization of mouse prefrontal cortex and neuronal subtypes regulating chronic pain
err2025-09-16
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errAritra Bhattacherjee; Chao Zhang; Brianna R. Watson; Mohamed Nadhir Djekidel; Jeffrey R. Moffitt; Yi Zhang
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Protocol optimization improves the performance of multiplexed RNA imaging
err2025-08-31
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errJosh J. Luce; Christian A. Reardon-Lochbaum; Paolo Cadinu; Rosalind J. Xu; Jose Aceves-Salvador; Evangelia Semizoglou; Bertrand Wong; Iris Lopez; Alan B. Cantor; William Renthal; Jeffrey R. Moffitt
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Inflammatory and anti-inflammatory cytokines bidirectionally modulate amygdala circuits regulating anxiety
errCELL
IF42.5
err2025-04-01
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PREAI
errLee, Byeongjun; Kwon, Jeong-Tae; Jeong, Yire; Caris, Hannah; Oh, Dongsun; Feng, Mengyang; Mejia, Irene Davila; Zhang, Xiaoying; Ishikawa, Tomoe; Watson, Brianna R.; Moffitt, Jeffrey R.; Chung, Kwanghun; Huh, Jun R.; Choi, Gloria B.
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Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning
err2024-05-01
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errLaubscher, Emily; Wang (Julie), Xuefei; Razin, Nitzan; Dougherty, Tom; Xu, Rosalind J.; Ombelets, Lincoln; Pao, Edward; Graf, William; Moffitt, Jeffrey R.; Yue, Yisong; Valen, David Van
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Spatial enrichment of the type 1 interferon signature in the brain of a neuropsychiatric lupus murine model (vol 114, pg 511, 2023)
err2024-02-01
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PREAI
errAw, Ernest; Zhang, Yingying; Yalcin, Esra; Herrmann, Uli; Lin, Stacie L.; Langston, Kent; Castrillon, Carlos; Ma, Minghe; Moffitt, Jeffrey R.; Carroll, Michael C.
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Spatial enrichment of the type 1 interferon signature in the brain of a neuropsychiatric lupus murine model
err2023-11-01
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errAw, Ernest; Zhang, Yingying; Yalcin, Esra; Herrmann, Uli; Lin, Stacie L.; Langston, Kent; Castrillon, Carlos; Ma, Minghe; Moffitt, Jeffrey R.; Carroll, Michael C.
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Spatial organization of the mouse retina at single cell resolution by MERFISH (14, 4929, 2023)
err2023-09-28
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errChoi, Jongsu; Li, Jin; Ferdous, Salma; Liang, Qingnan; Moffitt, Jeffrey R.; Chen, Rui
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Spatial organization of the mouse retina at single cell resolution by MERFISH
err2023-08-15
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errOAAI
errChoi, Jongsu; Li, Jin; Ferdous, Salma; Liang, Qingnan; Moffitt, Jeffrey R.; Chen, Rui
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Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)
err2023-07-19
err36
errOAAI
errJain, Sanjay; Pei, Liming; Spraggins, Jeffrey M.; Angelo, Michael; Carson, James P.; Gehlenborg, Nils; Ginty, Fiona; Goncalves, Joana P.; Hagood, James S.; Hickey, John W.; Kelleher, Neil L.; Laurent, Louise C.; Lin, Shin; Lin, Yiing; Liu, Huiping; Naba, Alexandra; Nakayasu, Ernesto S.; Qian, Wei-Jun; Radtke, Andrea; Robson, Paul; Stockwell, Brent R.; Van de Plas, Raf; Vlachos, Ioannis S.; Zhou, Mowei; Boerner, Katy; Snyder, Michael P.; Ahn, Kyung Jin; Allen, Jamie; Anderson, David M.; Anderton, Christopher R.; Curcio, Christine; Angelin, Alessia; Arvanitis, Constadina; Atta, Lyla; Awosika-Olumo, Demi; Bahmani, Amir; Bai, Huajun; Balderrama, Karol; Balzano, Leandro; Bandyopadhyay, Gautam; Bandyopadhyay, Shovik; Bar-Joseph, Ziv; Barnhart, Kurt; Barwinska, Daria; Becich, Michael; Becker, Laren; Becker, Winston; Bedi, Kenneth; Bendall, Sean; Benninger, Kathy; Betancur, David; Bettinger, Keith; Billings, Sunteasja; Blood, Philip; Bolin, Daniel; Border, Samuel; Bosse, Marc; Bramer, Lisa; Brewer, Maya; Brusko, Maigan; Bueckle, Andreas; Burke, Karl; Burnum-Johnson, Kristin; Butcher, Eugene; Butterworth, Elizabeth; Cai, Long; Calandrelli, Riccardo; Caldwell, Michael; Campbell-Thompson, Martha; Cao, Dongfeng; Cao-Berg, Ivan; Caprioli, Richard; Caraccio, Chiara; Caron, Anita; Carroll, Megan; Chadwick, Chrystal; Chen, Angela; Chen, Derek; Chen, Fei; Chen, Haoran; Chen, Jing; Chen, Li; Chen, Lu; Chiacchia, Kenneth; Cho, Sanghee; Chou, Peter; Choy, Lisa; Cisar, Cecilia; Clair, Geremy; Clarke, Laura; Clouthier, Kelly A.; Colley, Madeline E.; Conlon, Kristin; Conroy, John; Contrepois, Kevin; Corbett, Anthony; Corwin, Alex; Cotter, Daniel; Courtois, Elise; Cruz, Aaron; Csonka, Christopher; Czupil, Kimberley; Daiya, Vicky; Dale, Kali; Davanagere, Shakeel Ahamed; Dayao, Monica; de Caestecker, Mark P.; Decker, Aubrianna; Deems, Stephen; Degnan, David; Desai, Tushar; Deshpande, Vikrant; Deutsch, Gail; Devlin, Michelle; Diep, Dinh; Dodd, Carla; Donahue, Sean; Dong, Weixiu; Peixoto, Rafael dos Santos; Duffy, Michael; Dufresne, Martin; Duong, Thu Elizabeth; Dutra, Jennifer; Eadon, Michael T.; El-Achkar, Tarek M.; Enninful, Archibald; Eraslan, Gokcen; Eshelman, Diane; Espin-Perez, Almudena; Esplin, Edward D.; Esselman, Allison; Falo, Louis D.; Falo, Louis; Fan, Jean; Fan, Rong; Farrow, Melissa A.; Farzad, Negin; Favaro, Patricia; Fermin, Jamie; Filiz, Ferda; Filus, Shane; Fisch, Kathleen; Fisher, Eyal; Fisher, Stephen; Flowers, Katelyn; Flynn, William F.; Fogo, Agnes B.; Fu, Dongtao (Ann); Fulcher, James; Fung, Anthony; Furst, Derek; Gallant, Michael; Gao, Fu; Gao, Yu; Gaulton, Kyle; Gaut, Joseph P.; Gee, James; Ghag, Reetika R.; Ghazanfar, Shila; Ghose, Soumya; Gisch, Debora; Gold, Ilan; Gondalia, Aashay; Gorman, Brittney; Greenleaf, William; Greenwald, Noah; Gregory, Brian; Guo, Rong; Gupta, Rajat; Hakimian, Hunter; Haltom, Jeff; Halushka, Marc; Han, Kyu Sang; Hanson, Casey; Harbury, Pehr; Hardi, Josef; Harlan, Linda; Harris, Raymond C.; Hartman, Austin; Heidari, Elyas; Helfer, Jesse; Helminiak, David; Hemberg, Martin; Henning, Nathaniel; Herr, Bruce W., II; Ho, Jonhan; Holden-Wiltse, Jeanne; Hong, Seung-Hyun; Hong, Young-Kwon; Honick, Brendan; Hood, Greg; Hu, Po; Hu, Qiwen; Huang, Molly; Huyck, Heidie; Imtiaz, Tamjid; Isberg, Olof Gerdur; Itkin, Maxim; Jackson, Dana; Jacobs, Marni; Jain, Yashvardhan; Jewell, David; Jiang, Lihua; Jiang, Zhenghui G.; Johnston, Sarah; Joshi, Pujan; Ju, Yingnan; Judd, Audra; Kagel, Adam; Kahn, Ari; Kalavros, Nikolaos; Kalhor, Kian; Karagkouni, Dimitra; Karathanos, Thomas; Karunamurthy, Arivarasan; Katari, Suhas; Kates, Heather; Kaushal, Madhurima; Keener, Nicholas; Keller, Mark; Kenney, Mariah; Kern, Colin; Kharchenko, Peter; Kim, Junhyong; Kingsford, Carl; Kirwan, Jessica; Kiselev, Vladimir; Kishi, Jocelyn; Kitata, Reta Birhanu; Knoten, Amanda; Kollar, Charles; Krishnamoorthy, Praveen; Kruse, Angela R. S.; Da, Kuang; Kundaje, Anshul; Kutschera, Eric; Kwon, Yumi; Lake, Blue B.; Lancaster, Samuel; Langlieb, Jonah; Lardenoije, Roy; Laronda, Monica; Laskin, Julia; Lau, Ken; Lee, Hayan; Lee, Maria; Lee, Mejeong; Strekalova, Yulia Levites; Li, Dongshunyi; Li, Jennifer; Li, Jilong; Li, Xiangtang; Li, Zhi; Liao, Yen-Chen; Liaw, Tiffany; Lin, Pei; Lin, Yulieh; Lindsay, Scott; Liu, Chunjie; Liu, Yang; Liu, Yuan; Lott, Marie; Lotz, Martin; Lowery, Lisa; Lu, Peiran; Lu, Xinyue; Lucarelli, Nicholas; Lun, Xiaokang; Luo, Zhifei; Ma, Jian; Macosko, Evan; Mahajan, Mayank; Maier, Libby; Makowski, Danika; Malek, Morad; Manthey, David; Manz, Trevor; Margulies, Kenneth; Marioni, John; Martindale, Matthew; Mason, Cayla; Mathews, Clayton; Maye, Peter; McCallum, Chuck; McDonough, Elizabeth; McDonough, Liz; Mcdowell, Hannah; Meads, Morgan; Medina-Serpas, Miguel; Ferreira, Ricardo Melo; Messinger, Jeffrey; Metis, Kay; Migas, Lukasz G.; Miller, Brendan; Mimar, Sayat; Minor, Brittany; Misra, Ravi; Missarova, Alsu; Mistretta, Christopher; Moens, Roger; Moerth, Eric; Moffitt, Jeffrey; Molla, Gesmira; Monroe, Matthew; Monte, Emma; Morgan, Mike; Muraro, Daniele; Murphy, Bob (Robert); Murray, Evan; Musen, Mark A.; Naglah, Ahmed; Nasamran, Chanond; Neelakantan, Taruna; Nevins, Stephanie; Hieu Nguyen; Nam Nguyen; Tram Nguyen; Tri Nguyen; Nigra, Deb; Nofal, Michel; Nolan, Garry; Nwanne, Gerald; O'Connor, Martin; Okuda, Kenichi; Olmer, Merissa; O'Neill, Kathleen; Otaluka, Nancy; Pang, Minxing; Parast, Mana; Pasa-Tolic, Ljiljana; Paten, Benedict; Patterson, Nathan Heath; Peng, Ting; Phillips, Gesina; Pichavant, Mina; Piehowski, Paul; Pilner, Hannah; Pingry, Ellie; Pita-Juarez, Yered; Plevritis, Sylvia; Ploumakis, Athanasios; Pouch, Alison; Pryhuber, Gloria; Puerto, Juan; Qaurooni, Danial; Qin, Ling; Quardokus, Ellen M.; Rajbhandari, Presha; Rakow-Penner, Rebecca; Ramasamy, Ramalakshmi; Read, David; Record, Elizabeth G.; Reeves, David; Ricarte, Allyson; Rodriguez-Soto, Ana; Ropelewski, Alexander; Rosario, Jean; Roselkis, Morla-Adames; Rowe, David; Roy, Tarun Kanti; Ruffalo, Matt; Ruschman, Nancy; Sabo, Angela; Sachdev, Nina; Saka, Sinem; Salamon, Diane; Sarder, Pinaki; Sasaki, Hiroshi; Satija, Rahul; Saunders, Diane; Sawka, Riley; Schey, Kevin; Schlehlein, Heidi; Scholten, David; Schultz, Sarah; Schwartz, Lauren; Schwenk, Melissa; Scibek, Robin; Segre, Ayellet; Serrata, Matthew; Shands, Walter; Shen, Xiaotao; Shendure, Jay; Shephard, Holly; Shi, Lingyan; Shi, Tujin; Shin, Dong-Guk; Shirey, Bill; Sibilla, Max; Silber, Michal; Silverstein, Jonathan; Simmel, Derek; Simmons, Alan; Singhal, Dhruv; Sivajothi, Santhosh; Smits, Thomas; Soncin, Francesca; Song, Qi; Stanley, Valentina; Stuart, Tim; Su, Hanquan; Su, Pei; Sun, Xin; Surrette, Christine; Swahn, Hannah; Tan, Kai; Teichmann, Sarah; Tejomay, Abhiroop; Tellides, George; Thomas, Kathleen; Thomas, Tracey; Thompson, Marissa; Tian, Hua; Tideman, Leonoor; Trapnell, Cole; Tsai, Albert G.; Tsai, Chia-Feng; Tsai, Leo; Tsui, Elizabeth; Tsui, Tina; Tung, Jason; Turner, Morgan; Uranic, Jackie; Vaishnav, Eeshit Dhaval; Varra, Sricharan Reddy; Vaskivskyi, Vasyl; Velickovic, Dusan; Velickovic, Marija; Verheyden, Jamie; Waldrip, Jessica; Wallace, Douglas; Wan, Xueyi; Wang, Allen; Wang, Fusheng; Wang, Meng; Wang, Shuoshuo; Wang, Xuefei; Wasserfall, Clive; Wayne, Leonard; Webber, James; Weber, Griffin M.; Wei, Bei; Wei, Jian-Jun; Weimer, Annika; Welling, Joel; Wen, Xingzhao; Wen, Zishen; Williams, MacKenzie; Winfree, Seth; Winograd, Nicholas; Woodard, Abashai; Wright, Devin; Wu, Fan; Wu, Pei-Hsun; Wu, Qiuyang; Wu, Xiaodong; Xing, Yi; Xu, Tiangyang; Yang, Manxi; Yang, Mingyu; Yap, Joseph; Ye, Dong Hye; Yin, Peng; Yuan, Zhou; Yun, Chi (Jina); Zahraei, Ali; Zemaitis, Kevin; Zhang, Bo; Zhang, Caibin; Zhang, Chenyu; Zhang, Chi; Zhang, Kun; Zhang, Shiping; Zhang, Ted; Zhang, Yida; Zhao, Bingqing; Zhao, Wenxin; Zheng, Jia Wen; Zhong, Sheng; Zhu, Bokai; Zhu, Chenchen; Zhu, Diming; Zhu, Quan; Zhu, Ying
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The emerging landscape of spatial profiling technologies
err2022-07-20
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PREAI
errMoffitt, Jeffrey R.; Lundberg, Emma; Heyn, Holger
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Cell segmentation in imaging-based spatial transcriptomics
err2021-10-14
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PREAI
errPetukhov, Viktor; Xu, Rosalind J.; Soldatov, Ruslan A.; Cadinu, Paolo; Khodosevich, Konstantin; Moffitt, Jeffrey R.; Kharchenko, Peter, V
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Multiplexed detection of RNA using MERFISH and branched DNA amplification
err2019-05-22
err127
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errXia, Chenglong; Babcock, Hazen P.; Moffitt, Jeffrey R.; Zhuang, Xiaowei
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Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy
err2018-03-19
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errWang, Guiping; Moffitt, Jeffrey R.; Zhuang, Xiaowei
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High-throughput, image-based screening of pooled genetic-variant libraries
err2017-10-30
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errEmanuel, George; Moffitt, Jeffrey R.; Zhuang, Xiaowei
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Spatial Organization of Chromatin Domains and Compartments in Single Chromosomes
err2017-02-01
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errWang, Siyuan; Su, Jun-Han; Beliveau, Brian J.; Bintu, Bogdan; Moffitt, Jeffrey R.; Wu, Chao-ting; Zhuang, Xiaowei
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