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1.

SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9.

Schmidt, Nora; Ganskih, Sabina; Wei, Yuanjie; Gabel, Alexander; Zielinski, Sebastian; Keshishian, Hasmik; Lareau, Caleb A; Zimmermann, Liv; Makroczyova, Jana; Pearce, Cadence; Krey, Karsten; Hennig, Thomas; Stegmaier, Sebastian; Moyon, Lambert; Horlacher, Marc; Werner, Simone; Aydin, Jens; Olguin-Nava, Marco; Potabattula, Ramya; Kibe, Anuja; Dölken, Lars; Smyth, Redmond P; Caliskan, Neva; Marsico, Annalisa; Krempl, Christine; Bodem, Jochen; Pichlmair, Andreas; Carr, Steven A; Chlanda, Petr; Erhard, Florian; Munschauer, Mathias.

Cell ; 186(22): 4834-4850.e23, 2023 10 26.

Article in English | MEDLINE | ID: mdl-37794589

2.

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer.

Johnstone, Sarah E; Reyes, Alejandro; Qi, Yifeng; Adriaens, Carmen; Hegazi, Esmat; Pelka, Karin; Chen, Jonathan H; Zou, Luli S; Drier, Yotam; Hecht, Vivian; Shoresh, Noam; Selig, Martin K; Lareau, Caleb A; Iyer, Sowmya; Nguyen, Son C; Joyce, Eric F; Hacohen, Nir; Irizarry, Rafael A; Zhang, Bin; Aryee, Martin J; Bernstein, Bradley E.

Cell ; 182(6): 1474-1489.e23, 2020 09 17.

Article in English | MEDLINE | ID: mdl-32841603

3.

Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations.

Chen, Ming-Huei; Raffield, Laura M; Mousas, Abdou; Sakaue, Saori; Huffman, Jennifer E; Moscati, Arden; Trivedi, Bhavi; Jiang, Tao; Akbari, Parsa; Vuckovic, Dragana; Bao, Erik L; Zhong, Xue; Manansala, Regina; Laplante, Véronique; Chen, Minhui; Lo, Ken Sin; Qian, Huijun; Lareau, Caleb A; Beaudoin, Mélissa; Hunt, Karen A; Akiyama, Masato; Bartz, Traci M; Ben-Shlomo, Yoav; Beswick, Andrew; Bork-Jensen, Jette; Bottinger, Erwin P; Brody, Jennifer A; van Rooij, Frank J A; Chitrala, Kumaraswamynaidu; Cho, Kelly; Choquet, Hélène; Correa, Adolfo; Danesh, John; Di Angelantonio, Emanuele; Dimou, Niki; Ding, Jingzhong; Elliott, Paul; Esko, Tõnu; Evans, Michele K; Floyd, James S; Broer, Linda; Grarup, Niels; Guo, Michael H; Greinacher, Andreas; Haessler, Jeff; Hansen, Torben; Howson, Joanna M M; Huang, Qin Qin; Huang, Wei; Jorgenson, Eric.

Cell ; 182(5): 1198-1213.e14, 2020 09 03.

Article in English | MEDLINE | ID: mdl-32888493

4.

The Polygenic and Monogenic Basis of Blood Traits and Diseases.

Vuckovic, Dragana; Bao, Erik L; Akbari, Parsa; Lareau, Caleb A; Mousas, Abdou; Jiang, Tao; Chen, Ming-Huei; Raffield, Laura M; Tardaguila, Manuel; Huffman, Jennifer E; Ritchie, Scott C; Megy, Karyn; Ponstingl, Hannes; Penkett, Christopher J; Albers, Patrick K; Wigdor, Emilie M; Sakaue, Saori; Moscati, Arden; Manansala, Regina; Lo, Ken Sin; Qian, Huijun; Akiyama, Masato; Bartz, Traci M; Ben-Shlomo, Yoav; Beswick, Andrew; Bork-Jensen, Jette; Bottinger, Erwin P; Brody, Jennifer A; van Rooij, Frank J A; Chitrala, Kumaraswamy N; Wilson, Peter W F; Choquet, Hélène; Danesh, John; Di Angelantonio, Emanuele; Dimou, Niki; Ding, Jingzhong; Elliott, Paul; Esko, Tõnu; Evans, Michele K; Felix, Stephan B; Floyd, James S; Broer, Linda; Grarup, Niels; Guo, Michael H; Guo, Qi; Greinacher, Andreas; Haessler, Jeff; Hansen, Torben; Howson, Joanna M M; Huang, Wei.

Cell ; 182(5): 1214-1231.e11, 2020 09 03.

Article in English | MEDLINE | ID: mdl-32888494

5.

Clonal expansion and epigenetic inheritance of long-lasting NK cell memory.

Rückert, Timo; Lareau, Caleb A; Mashreghi, Mir-Farzin; Ludwig, Leif S; Romagnani, Chiara.

Nat Immunol ; 23(11): 1551-1563, 2022 Nov.

Article in English | MEDLINE | ID: mdl-36289449

6.

Runx3 drives a CD8⁺ T cell tissue residency program that is absent in CD4⁺ T cells.

Fonseca, Raíssa; Burn, Thomas N; Gandolfo, Luke C; Devi, Sapna; Park, Simone L; Obers, Andreas; Evrard, Maximilien; Christo, Susan N; Buquicchio, Frank A; Lareau, Caleb A; McDonald, Keely M; Sandford, Sarah K; Zamudio, Natasha M; Zanluqui, Nagela G; Zaid, Ali; Speed, Terence P; Satpathy, Ansuman T; Mueller, Scott N; Carbone, Francis R; Mackay, Laura K.

Nat Immunol ; 23(8): 1236-1245, 2022 08.

Article in English | MEDLINE | ID: mdl-35882933

7.

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics.

Ludwig, Leif S; Lareau, Caleb A; Ulirsch, Jacob C; Christian, Elena; Muus, Christoph; Li, Lauren H; Pelka, Karin; Ge, Will; Oren, Yaara; Brack, Alison; Law, Travis; Rodman, Christopher; Chen, Jonathan H; Boland, Genevieve M; Hacohen, Nir; Rozenblatt-Rosen, Orit; Aryee, Martin J; Buenrostro, Jason D; Regev, Aviv; Sankaran, Vijay G.

Cell ; 176(6): 1325-1339.e22, 2019 03 07.

Article in English | MEDLINE | ID: mdl-30827679

8.

The cis-Regulatory Atlas of the Mouse Immune System.

Yoshida, Hideyuki; Lareau, Caleb A; Ramirez, Ricardo N; Rose, Samuel A; Maier, Barbara; Wroblewska, Aleksandra; Desland, Fiona; Chudnovskiy, Aleksey; Mortha, Arthur; Dominguez, Claudia; Tellier, Julie; Kim, Edy; Dwyer, Dan; Shinton, Susan; Nabekura, Tsukasa; Qi, YiLin; Yu, Bingfei; Robinette, Michelle; Kim, Ki-Wook; Wagers, Amy; Rhoads, Andrew; Nutt, Stephen L; Brown, Brian D; Mostafavi, Sara; Buenrostro, Jason D; Benoist, Christophe.

Cell ; 176(4): 897-912.e20, 2019 02 07.

Article in English | MEDLINE | ID: mdl-30686579

9.

A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification.

Liu, Chunhong; Nagashima, Hiroyuki; Fernando, Nilisha; Bass, Victor; Gopalakrishnan, Jaanam; Signorella, Sadie; Montgomery, Will; Lim, Ai Ing; Harrison, Oliver; Reich, Lauren; Yao, Chen; Sun, Hong-Wei; Brooks, Stephen R; Jiang, Kan; Nagarajan, Vijayaraj; Zhao, Yongbing; Jung, Seolkyoung; Phillips, Rachael; Mikami, Yohei; Lareau, Caleb A; Kanno, Yuka; Jankovic, Dragana; Aryee, Martin J; Pekowska, Aleksandra; Belkaid, Yasmine; O'Shea, John; Shih, Han-Yu.

Immunity ; 57(5): 1005-1018.e7, 2024 May 14.

Article in English | MEDLINE | ID: mdl-38697116

10.

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.

Buenrostro, Jason D; Corces, M Ryan; Lareau, Caleb A; Wu, Beijing; Schep, Alicia N; Aryee, Martin J; Majeti, Ravindra; Chang, Howard Y; Greenleaf, William J.

Cell ; 173(6): 1535-1548.e16, 2018 05 31.

Article in English | MEDLINE | ID: mdl-29706549

11.

Distinct Foxp3 enhancer elements coordinate development, maintenance, and function of regulatory T cells.

Kawakami, Ryoji; Kitagawa, Yohko; Chen, Kelvin Y; Arai, Masaya; Ohara, Daiya; Nakamura, Yamami; Yasuda, Keiko; Osaki, Motonao; Mikami, Norihisa; Lareau, Caleb A; Watanabe, Hitomi; Kondoh, Gen; Hirota, Keiji; Ohkura, Naganari; Sakaguchi, Shimon.

Immunity ; 54(5): 947-961.e8, 2021 05 11.

Article in English | MEDLINE | ID: mdl-33930308

12.

FOXO1 is a master regulator of memory programming in CAR T cells.

Doan, Alexander E; Mueller, Katherine P; Chen, Andy Y; Rouin, Geoffrey T; Chen, Yingshi; Daniel, Bence; Lattin, John; Markovska, Martina; Mozarsky, Brett; Arias-Umana, Jose; Hapke, Robert; Jung, In-Young; Wang, Alice; Xu, Peng; Klysz, Dorota; Zuern, Gabrielle; Bashti, Malek; Quinn, Patrick J; Miao, Zhuang; Sandor, Katalin; Zhang, Wenxi; Chen, Gregory M; Ryu, Faith; Logun, Meghan; Hall, Junior; Tan, Kai; Grupp, Stephan A; McClory, Susan E; Lareau, Caleb A; Fraietta, Joseph A; Sotillo, Elena; Satpathy, Ansuman T; Mackall, Crystal L; Weber, Evan W.

Nature ; 629(8010): 211-218, 2024 May.

Article in English | MEDLINE | ID: mdl-38600391

13.

Latent human herpesvirus 6 is reactivated in CAR T cells.

Lareau, Caleb A; Yin, Yajie; Maurer, Katie; Sandor, Katalin D; Daniel, Bence; Yagnik, Garima; Peña, José; Crawford, Jeremy Chase; Spanjaart, Anne M; Gutierrez, Jacob C; Haradhvala, Nicholas J; Riberdy, Janice M; Abay, Tsion; Stickels, Robert R; Verboon, Jeffrey M; Liu, Vincent; Buquicchio, Frank A; Wang, Fangyi; Southard, Jackson; Song, Ren; Li, Wenjing; Shrestha, Aastha; Parida, Laxmi; Getz, Gad; Maus, Marcela V; Li, Shuqiang; Moore, Alison; Roberts, Zachary J; Ludwig, Leif S; Talleur, Aimee C; Thomas, Paul G; Dehghani, Houman; Pertel, Thomas; Kundaje, Anshul; Gottschalk, Stephen; Roth, Theodore L; Kersten, Marie J; Wu, Catherine J; Majzner, Robbie G; Satpathy, Ansuman T.

Nature ; 623(7987): 608-615, 2023 Nov.

Article in English | MEDLINE | ID: mdl-37938768

14.

Spatial genomics enables multi-modal study of clonal heterogeneity in tissues.

Zhao, Tongtong; Chiang, Zachary D; Morriss, Julia W; LaFave, Lindsay M; Murray, Evan M; Del Priore, Isabella; Meli, Kevin; Lareau, Caleb A; Nadaf, Naeem M; Li, Jilong; Earl, Andrew S; Macosko, Evan Z; Jacks, Tyler; Buenrostro, Jason D; Chen, Fei.

Nature ; 601(7891): 85-91, 2022 01.

Article in English | MEDLINE | ID: mdl-34912115

15.

A RORÎ³t⁺ cell instructs gut microbiota-specific T_reg cell differentiation.

Kedmi, Ranit; Najar, Tariq A; Mesa, Kailin R; Grayson, Allyssa; Kroehling, Lina; Hao, Yuhan; Hao, Stephanie; Pokrovskii, Maria; Xu, Mo; Talbot, Jhimmy; Wang, Jiaxi; Germino, Joe; Lareau, Caleb A; Satpathy, Ansuman T; Anderson, Mark S; Laufer, Terri M; Aifantis, Iannis; Bartleson, Juliet M; Allen, Paul M; Paidassi, Helena; Gardner, James M; Stoeckius, Marlon; Littman, Dan R.

Nature ; 610(7933): 737-743, 2022 10.

Article in English | MEDLINE | ID: mdl-36071167

16.

An old BATF's new T-ricks.

Lareau, Caleb A; Satpathy, Ansuman T.

Nat Immunol ; 21(11): 1309-1310, 2020 11.

Article in English | MEDLINE | ID: mdl-32989330

17.

Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells.

Bao, Erik L; Nandakumar, Satish K; Liao, Xiaotian; Bick, Alexander G; Karjalainen, Juha; Tabaka, Marcin; Gan, Olga I; Havulinna, Aki S; Kiiskinen, Tuomo T J; Lareau, Caleb A; de Lapuente Portilla, Aitzkoa L; Li, Bo; Emdin, Connor; Codd, Veryan; Nelson, Christopher P; Walker, Christopher J; Churchhouse, Claire; de la Chapelle, Albert; Klein, Daryl E; Nilsson, Björn; Wilson, Peter W F; Cho, Kelly; Pyarajan, Saiju; Gaziano, J Michael; Samani, Nilesh J; Regev, Aviv; Palotie, Aarno; Neale, Benjamin M; Dick, John E; Natarajan, Pradeep; O'Donnell, Christopher J; Daly, Mark J; Milyavsky, Michael; Kathiresan, Sekar; Sankaran, Vijay G.

Nature ; 586(7831): 769-775, 2020 10.

Article in English | MEDLINE | ID: mdl-33057200

18.

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors.

Grünewald, Julian; Zhou, Ronghao; Garcia, Sara P; Iyer, Sowmya; Lareau, Caleb A; Aryee, Martin J; Joung, J Keith.

Nature ; 569(7756): 433-437, 2019 05.

Article in English | MEDLINE | ID: mdl-30995674

19.

Publisher Correction: FOXO1 is a master regulator of memory programming in CAR T cells.

Doan, Alexander E; Mueller, Katherine P; Chen, Andy Y; Rouin, Geoffrey T; Chen, Yingshi; Daniel, Bence; Lattin, John; Markovska, Martina; Mozarsky, Brett; Arias-Umana, Jose; Hapke, Robert; Jung, In-Young; Wang, Alice; Xu, Peng; Klysz, Dorota; Zuern, Gabrielle; Bashti, Malek; Quinn, Patrick J; Miao, Zhuang; Sandor, Katalin; Zhang, Wenxi; Chen, Gregory M; Ryu, Faith; Logun, Meghan; Hall, Junior; Tan, Kai; Grupp, Stephan A; McClory, Susan E; Lareau, Caleb A; Fraietta, Joseph A; Sotillo, Elena; Satpathy, Ansuman T; Mackall, Crystal L; Weber, Evan W.

Nature ; 629(8011): E11, 2024 May.

Article in English | MEDLINE | ID: mdl-38654101

20.

Single-cell chromatin state analysis with Signac.

Stuart, Tim; Srivastava, Avi; Madad, Shaista; Lareau, Caleb A; Satija, Rahul.

Nat Methods ; 18(11): 1333-1341, 2021 11.

Article in English | MEDLINE | ID: mdl-34725479

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