Aviv Regev (A Regev)

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 138

Top Venues

Nature biotechnology

Nature communications

Nature

Science (New York, N.Y.)

This page only lists publications with an associated author ORCID identifier.

Publications

Masashi Fujita, Zongmei Gao, Lu Zeng, Cristin McCabe, Charles C White, Bernard Ng, Gilad Sahar Green, Orit Rozenblatt-Rosen, Devan Phillips, Liat Amir-Zilberstein, Hyo Lee, Richard V Pearse, Atlas Khan, Badri N Vardarajan, Krzysztof Kiryluk, Chun Jimmie Ye, Hans-Ulrich Klein, Gao Wang, Aviv Regev, Naomi Habib, Julie A Schneider, Yangling Wang, Tracy L Young-Pearse, Sara Mostafavi, David A Bennett, Vilas Menon, Philip Lawrence De Jager
Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain. Nature genetics 56 (4) (2024)
Anand G Patel, Orr Ashenberg, Natalie B Collins, Åsa Segerstolpe, Sizun J Jiang, Michal Slyper, Xin Huang, Chiara Caraccio, Hongjian Jin, Heather S Sheppard, Ke Xu, Ti-Cheng Chang, Brent A Orr, Abbas Shirinifard, Richard H Chapple, Amber Shen, Michael R Clay, Ruth G Tatevossian, Colleen Reilly, Jaimin Patel, Marybeth Lupo, Cynthia Cline, Danielle Dionne, Caroline B M Porter, Julia Waldman, Yunhao Bai, Bokai Zhu, Irving Barrera, Evan Murray, Sébastien Vigneau, Sara Napolitano, Isaac Wakiro, Jingyi Wu, Grace Grimaldi, Laura Dellostritto, Karla Helvie, Asaf Rotem, Ana Lako, Nicole Cullen, Kathleen L Pfaff, Åsa Karlström, Judit Jané-Valbuena, Ellen Z Todres, Aaron Thorner, Paul Geeleher, Scott J Rodig, Xin Zhou, Elizabeth Stewart, Bruce E Johnson, Gang Wu, Fei Chen, Jiyang Yu, Yury Goltsev, Garry P Nolan, Orit Rozenblatt-Rosen, Aviv Regev, Michael A Dyer
A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity. bioRxiv : the preprint server for biology (2024)
Sean K Simmons, Xian Adiconis, Nathan Haywood, Jacob Parker, Zechuan Lin, Zhixiang Liao, Idil Tuncali, Aziz M Al'Khafaji, Asa Shin, Karthik A Jagadeesh, Kirk Gosik, Michael Gatzen, Jonathan T Smith, Daniel N El Kodsi, Yuliya Kuras, Clare Baecher-Allan, Geidy E Serrano, Thomas G Beach, Kiran V Garimella, Orit Rozenblatt-Rosen, Aviv Regev, Xianjun Dong, Clemens R Scherzer, Joshua Z Levin
Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data. bioRxiv : the preprint server for biology (2024)
Jiarui Ding, John J Garber, Amiko Uchida, Ariel Lefkovith, Grace T Carter, Praveen Vimalathas, Lauren Canha, Michael Dougan, Kyle Staller, Joseph Yarze, Toni Marie Delorey, Orit Rozenblatt-Rosen, Orr Ashenberg, Daniel B Graham, Jacques Deguine, Aviv Regev, Ramnik J Xavier
An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission. Nature communications 15 (1) (2024)
Jiarui Ding, John J Garber, Amiko Uchida, Ariel Lefkovith, Grace T Carter, Praveen Vimalathas, Lauren Canha, Michael Dougan, Kyle Staller, Joseph Yarze, Toni Marie Delorey, Orit Rozenblatt-Rosen, Orr Ashenberg, Daniel B Graham, Jacques Deguine, Aviv Regev, Ramnik J Xavier
An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission. Nature communications 15 (1) (2024)
Koseki J Kobayashi-Kirschvink, Charles S Comiter, Shreya Gaddam, Taylor Joren, Emanuelle I Grody, Johain R Ounadjela, Ke Zhang, Baoliang Ge, Jeon Woong Kang, Ramnik J Xavier, Peter T C So, Tommaso Biancalani, Jian Shu, Aviv Regev
Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA. Nature biotechnology (2024)
Masashi Fujita, Zongmei Gao, Lu Zeng, Cristin McCabe, Charles C White, Bernard Ng, Gilad Sahar Green, Orit Rozenblatt-Rosen, Devan Phillips, Liat Amir-Zilberstein, Hyo Lee, Richard V Pearse, Atlas Khan, Badri N Vardarajan, Krzysztof Kiryluk, Chun Jimmie Ye, Hans-Ulrich Klein, Gao Wang, Aviv Regev, Naomi Habib, Julie A Schneider, Yangling Wang, Tracy L Young-Pearse, Sara Mostafavi, David A Bennett, Vilas Menon, Philip Lawrence De Jager
Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain. Nature genetics (2024)
Koseki J Kobayashi-Kirschvink, Charles S Comiter, Shreya Gaddam, Taylor Joren, Emanuelle I Grody, Johain R Ounadjela, Ke Zhang, Baoliang Ge, Jeon Woong Kang, Ramnik J Xavier, Peter T C So, Tommaso Biancalani, Jian Shu, Aviv Regev
Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA. Nature biotechnology (2024)
Sean K Simmons, Xian Adiconis, Nathan Haywood, Jacob Parker, Zechuan Lin, Zhixiang Liao, Idil Tuncali, Aziz M Al'Khafaji, Asa Shin, Karthik A Jagadeesh, Kirk Gosik, Michael Gatzen, Jonathan T Smith, Daniel N El Kodsi, Yuliya Kuras, Clare Baecher-Allan, Geidy E Serrano, Thomas G Beach, Kiran V Garimella, Orit Rozenblatt-Rosen, Aviv Regev, Xianjun Dong, Clemens R Scherzer, Joshua Z Levin
Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data. bioRxiv : the preprint server for biology (2024)
Jiarui Ding, John J Garber, Amiko Uchida, Ariel Lefkovith, Grace T Carter, Praveen Vimalathas, Lauren Canha, Michael Dougan, Kyle Staller, Joseph Yarze, Toni Marie Delorey, Orit Rozenblatt-Rosen, Orr Ashenberg, Daniel B Graham, Jacques Deguine, Aviv Regev, Ramnik J Xavier
An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission. Nature communications 15 (1) (2024)
Koseki J Kobayashi-Kirschvink, Charles S Comiter, Shreya Gaddam, Taylor Joren, Emanuelle I Grody, Johain R Ounadjela, Ke Zhang, Baoliang Ge, Jeon Woong Kang, Ramnik J Xavier, Peter T C So, Tommaso Biancalani, Jian Shu, Aviv Regev
Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA. Nature biotechnology (2024)
Lior Fishman, Avani Modak, Gal Nechooshtan, Talya Razin, Florian Erhard, Aviv Regev, Jeffrey A Farrell, Michal Rabani
Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq. Nature communications 15 (1) (2024)
Pratiksha I Thakore, Alexandra Schnell, Linglin Huang, Maryann Zhao, Yu Hou, Elena Christian, Sarah Zaghouani, Chao Wang, Vasundhara Singh, Anvita Singaraju, Rajesh Kumar Krishnan, Deneen Kozoriz, Sai Ma, Venkat Sankar, Samuele Notarbartolo, Jason D Buenrostro, Federica Sallusto, Nikolaos A Patsopoulos, Orit Rozenblatt-Rosen, Vijay K Kuchroo, Aviv Regev
BACH2 regulates diversification of regulatory and proinflammatory chromatin states in T H 17 cells. Nature immunology 25 (8) (2024)
Lior Fishman, Avani Modak, Gal Nechooshtan, Talya Razin, Florian Erhard, Aviv Regev, Jeffrey A Farrell, Michal Rabani
Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq. Nature communications 15 (1) (2024)
Lior Fishman, Avani Modak, Gal Nechooshtan, Talya Razin, Florian Erhard, Aviv Regev, Jeffrey A Farrell, Michal Rabani
Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq. Nature communications 15 (1) (2024)
Koseki J Kobayashi-Kirschvink, Charles S Comiter, Shreya Gaddam, Taylor Joren, Emanuelle I Grody, Johain R Ounadjela, Ke Zhang, Baoliang Ge, Jeon Woong Kang, Ramnik J Xavier, Peter T C So, Tommaso Biancalani, Jian Shu, Aviv Regev
Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA. Nature biotechnology (2024)
Jiarui Ding, John J Garber, Amiko Uchida, Ariel Lefkovith, Grace T Carter, Praveen Vimalathas, Lauren Canha, Michael Dougan, Kyle Staller, Joseph Yarze, Toni Marie Delorey, Orit Rozenblatt-Rosen, Orr Ashenberg, Daniel B Graham, Jacques Deguine, Aviv Regev, Ramnik J Xavier
An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission. Nature communications 15 (1) (2024)
Anand G Patel, Orr Ashenberg, Natalie B Collins, Åsa Segerstolpe, Sizun J Jiang, Michal Slyper, Xin Huang, Chiara Caraccio, Hongjian Jin, Heather S Sheppard, Ke Xu, Ti-Cheng Chang, Brent A Orr, Abbas Shirinifard, Richard H Chapple, Amber Shen, Michael R Clay, Ruth G Tatevossian, Colleen Reilly, Jaimin Patel, Marybeth Lupo, Cynthia Cline, Danielle Dionne, Caroline B M Porter, Julia Waldman, Yunhao Bai, Bokai Zhu, Irving Barrera, Evan Murray, Sébastien Vigneau, Sara Napolitano, Isaac Wakiro, Jingyi Wu, Grace Grimaldi, Laura Dellostritto, Karla Helvie, Asaf Rotem, Ana Lako, Nicole Cullen, Kathleen L Pfaff, Åsa Karlström, Judit Jané-Valbuena, Ellen Z Todres, Aaron Thorner, Paul Geeleher, Scott J Rodig, Xin Zhou, Elizabeth Stewart, Bruce E Johnson, Gang Wu, Fei Chen, Jiyang Yu, Yury Goltsev, Garry P Nolan, Orit Rozenblatt-Rosen, Aviv Regev, Michael A Dyer
A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity. bioRxiv : the preprint server for biology (2024)
Masashi Fujita, Zongmei Gao, Lu Zeng, Cristin McCabe, Charles C White, Bernard Ng, Gilad Sahar Green, Orit Rozenblatt-Rosen, Devan Phillips, Liat Amir-Zilberstein, Hyo Lee, Richard V Pearse, Atlas Khan, Badri N Vardarajan, Krzysztof Kiryluk, Chun Jimmie Ye, Hans-Ulrich Klein, Gao Wang, Aviv Regev, Naomi Habib, Julie A Schneider, Yangling Wang, Tracy L Young-Pearse, Sara Mostafavi, David A Bennett, Vilas Menon, Philip Lawrence De Jager
Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain. Nature genetics 56 (4) (2024)
Anand G Patel, Orr Ashenberg, Natalie B Collins, Åsa Segerstolpe, Sizun J Jiang, Michal Slyper, Xin Huang, Chiara Caraccio, Hongjian Jin, Heather S Sheppard, Ke Xu, Ti-Cheng Chang, Brent A Orr, Abbas Shirinifard, Richard H Chapple, Amber Shen, Michael R Clay, Ruth G Tatevossian, Colleen Reilly, Jaimin Patel, Marybeth Lupo, Cynthia Cline, Danielle Dionne, Caroline B M Porter, Julia Waldman, Yunhao Bai, Bokai Zhu, Irving Barrera, Evan Murray, Sébastien Vigneau, Sara Napolitano, Isaac Wakiro, Jingyi Wu, Grace Grimaldi, Laura Dellostritto, Karla Helvie, Asaf Rotem, Ana Lako, Nicole Cullen, Kathleen L Pfaff, Åsa Karlström, Judit Jané-Valbuena, Ellen Z Todres, Aaron Thorner, Paul Geeleher, Scott J Rodig, Xin Zhou, Elizabeth Stewart, Bruce E Johnson, Gang Wu, Fei Chen, Jiyang Yu, Yury Goltsev, Garry P Nolan, Orit Rozenblatt-Rosen, Aviv Regev, Michael A Dyer
A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity. bioRxiv : the preprint server for biology (2024)
Masashi Fujita, Zongmei Gao, Lu Zeng, Cristin McCabe, Charles C White, Bernard Ng, Gilad Sahar Green, Orit Rozenblatt-Rosen, Devan Phillips, Liat Amir-Zilberstein, Hyo Lee, Richard V Pearse, Atlas Khan, Badri N Vardarajan, Krzysztof Kiryluk, Chun Jimmie Ye, Hans-Ulrich Klein, Gao Wang, Aviv Regev, Naomi Habib, Julie A Schneider, Yangling Wang, Tracy L Young-Pearse, Sara Mostafavi, David A Bennett, Vilas Menon, Philip Lawrence De Jager
Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain. Nature genetics 56 (4) (2024)
Jiarui Ding, John J Garber, Amiko Uchida, Ariel Lefkovith, Grace T Carter, Praveen Vimalathas, Lauren Canha, Michael Dougan, Kyle Staller, Joseph Yarze, Toni Marie Delorey, Orit Rozenblatt-Rosen, Orr Ashenberg, Daniel B Graham, Jacques Deguine, Aviv Regev, Ramnik J Xavier
An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission. Nature communications 15 (1) (2024)
Adam J Rubin, Tyler T Dao, Amelia V Schueppert, Aviv Regev, Alex K Shalek
LAT encodes T cell activation pathway balance. bioRxiv : the preprint server for biology (2024)
Koseki J Kobayashi-Kirschvink, Charles S Comiter, Shreya Gaddam, Taylor Joren, Emanuelle I Grody, Johain R Ounadjela, Ke Zhang, Baoliang Ge, Jeon Woong Kang, Ramnik J Xavier, Peter T C So, Tommaso Biancalani, Jian Shu, Aviv Regev
Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA. Nature biotechnology (2024)
Pratiksha I Thakore, Alexandra Schnell, Linglin Huang, Maryann Zhao, Yu Hou, Elena Christian, Sarah Zaghouani, Chao Wang, Vasundhara Singh, Anvita Singaraju, Rajesh Kumar Krishnan, Deneen Kozoriz, Sai Ma, Venkat Sankar, Samuele Notarbartolo, Jason D Buenrostro, Federica Sallusto, Nikolaos A Patsopoulos, Orit Rozenblatt-Rosen, Vijay K Kuchroo, Aviv Regev
BACH2 regulates diversification of regulatory and proinflammatory chromatin states in T H 17 cells. Nature immunology 25 (8) (2024)
Pratiksha I Thakore, Alexandra Schnell, Linglin Huang, Maryann Zhao, Yu Hou, Elena Christian, Sarah Zaghouani, Chao Wang, Vasundhara Singh, Anvita Singaraju, Rajesh Kumar Krishnan, Deneen Kozoriz, Sai Ma, Venkat Sankar, Samuele Notarbartolo, Jason D Buenrostro, Federica Sallusto, Nikolaos A Patsopoulos, Orit Rozenblatt-Rosen, Vijay K Kuchroo, Aviv Regev
BACH2 regulates diversification of regulatory and proinflammatory chromatin states in T H 17 cells. Nature immunology (2024)
Lior Fishman, Avani Modak, Gal Nechooshtan, Talya Razin, Florian Erhard, Aviv Regev, Jeffrey A Farrell, Michal Rabani
Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq. Nature communications 15 (1) (2024)
Pratiksha I Thakore, Alexandra Schnell, Linglin Huang, Maryann Zhao, Yu Hou, Elena Christian, Sarah Zaghouani, Chao Wang, Vasundhara Singh, Anvita Singaraju, Rajesh Kumar Krishnan, Deneen Kozoriz, Sai Ma, Venkat Sankar, Samuele Notarbartolo, Jason D Buenrostro, Federica Sallusto, Nikolaos A Patsopoulos, Orit Rozenblatt-Rosen, Vijay K Kuchroo, Aviv Regev
BACH2 regulates diversification of regulatory and proinflammatory chromatin states in T H 17 cells. Nature immunology (2024)
Johannes F Scheid, Basak Eraslan, Andrew Hudak, Eric M Brown, Dallis Sergio, Toni Marie Delorey, Devan Phillips, Ariel Lefkovith, Alison T Jess, Lennard W Duck, Charles O Elson, Hera Vlamakis, Damian Rafal Plichta, Jacques Deguine, Ashwin N Ananthakrishnan, Daniel B Graham, Aviv Regev, Ramnik J Xavier
Remodeling of colon plasma cell repertoire within ulcerative colitis patients. The Journal of experimental medicine 220 (4) (2023)
Methodios Ximerakis, Kristina M Holton, Richard M Giadone, Ceren Ozek, Monika Saxena, Samara Santiago, Xian Adiconis, Danielle Dionne, Lan Nguyen, Kavya M Shah, Jill M Goldstein, Caterina Gasperini, Ioannis A Gampierakis, Scott L Lipnick, Sean K Simmons, Sean M Buchanan, Amy J Wagers, Aviv Regev, Joshua Z Levin, Lee L Rubin
Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types. Nature aging 3 (3) (2023)
Ethan A G Baker, Denis Schapiro, Bianca Dumitrascu, Sanja Vickovic, Aviv Regev
In silico tissue generation and power analysis for spatial omics. Nature methods 20 (3) (2023)
Anael Cain, Mariko Taga, Cristin McCabe, Gilad S Green, Idan Hekselman, Charles C White, Dylan I Lee, Pallavi Gaur, Orit Rozenblatt-Rosen, Feng Zhang, Esti Yeger-Lotem, David A Bennett, Hyun-Sik Yang, Aviv Regev, Vilas Menon, Naomi Habib, Philip Lawrence De Jager
Multicellular communities are perturbed in the aging human brain and Alzheimer's disease. Nature neuroscience (2023)
Britta Lötstedt, Martin Stražar, Ramnik Xavier, Aviv Regev, Sanja Vickovic
Spatial host-microbiome sequencing reveals niches in the mouse gut. Nature biotechnology (2023)
Methodios Ximerakis, Kristina M Holton, Richard M Giadone, Ceren Ozek, Monika Saxena, Samara Santiago, Xian Adiconis, Danielle Dionne, Lan Nguyen, Kavya M Shah, Jill M Goldstein, Caterina Gasperini, Ioannis A Gampierakis, Scott L Lipnick, Sean K Simmons, Sean M Buchanan, Amy J Wagers, Aviv Regev, Joshua Z Levin, Lee L Rubin
Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types. Nature aging 3 (3) (2023)
Methodios Ximerakis, Kristina M Holton, Richard M Giadone, Ceren Ozek, Monika Saxena, Samara Santiago, Xian Adiconis, Danielle Dionne, Lan Nguyen, Kavya M Shah, Jill M Goldstein, Caterina Gasperini, Ioannis A Gampierakis, Scott L Lipnick, Sean K Simmons, Sean M Buchanan, Amy J Wagers, Aviv Regev, Joshua Z Levin, Lee L Rubin
Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types. Nature aging 3 (3) (2023)
Methodios Ximerakis, Kristina M Holton, Richard M Giadone, Ceren Ozek, Monika Saxena, Samara Santiago, Xian Adiconis, Danielle Dionne, Lan Nguyen, Kavya M Shah, Jill M Goldstein, Caterina Gasperini, Ioannis A Gampierakis, Scott L Lipnick, Sean K Simmons, Sean M Buchanan, Amy J Wagers, Aviv Regev, Joshua Z Levin, Lee L Rubin
Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types. Nature aging 3 (3) (2023)
Ethan A G Baker, Denis Schapiro, Bianca Dumitrascu, Sanja Vickovic, Aviv Regev
In silico tissue generation and power analysis for spatial omics. Nature methods (2023)
Ethan A G Baker, Denis Schapiro, Bianca Dumitrascu, Sanja Vickovic, Aviv Regev
In silico tissue generation and power analysis for spatial omics. Nature methods 20 (3) (2023)
Davide Placido, Bo Yuan, Jessica X Hjaltelin, Chunlei Zheng, Amalie Dahl Haue, Piotr J Chmura, Chen Yuan, Jihye Kim, Renato Umeton, Gregory Antell, Alexander Chowdhury, Alexandra Franz, Lauren Brais, Elizabeth Andrews, Debora S Marks, Aviv Regev, Siamack Ayandeh, Mary T Brophy, Nhan V Do, Peter Kraft, Brian M Wolpin, Michael H Rosenthal, Nathanael R Fillmore, Soren Brunak, Chris Sander
A deep learning algorithm to predict risk of pancreatic cancer from disease trajectories. Nature medicine 29 (5) (2023)
Caleb A Lareau, Sonia M Dubois, Frank A Buquicchio, Yu-Hsin Hsieh, Kopal Garg, Pauline Kautz, Lena Nitsch, Samantha D Praktiknjo, Patrick Maschmeyer, Jeffrey M Verboon, Jacob C Gutierrez, Yajie Yin, Evgenij Fiskin, Wendy Luo, Eleni P Mimitou, Christoph Muus, Rhea Malhotra, Sumit Parikh, Mark Daniel Fleming, Lena Oevermann, Johannes Hubertus Schulte, Cornelia Eckert, Anshul Kundaje, Peter Smibert, Santosha A Vardhana, Ansuman T Satpathy, Aviv Regev, Vijay G Sankaran, Suneet Agarwal, Leif S Ludwig
Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells. Nature genetics (2023)
Elle M Weeks, Jacob C Ulirsch, Nathan Y Cheng, Brian L Trippe, Rebecca S Fine, Jenkai Miao, Tejal A Patwardhan, Masahiro Kanai, Joseph Nasser, Charles P Fulco, Katherine C Tashman, François Aguet, Taibo Li, Jose Ordovas-Montanes, Christopher S Smillie, Moshe Biton, Alex K Shalek, Ashwin N Ananthakrishnan, Ramnik J Xavier, Aviv Regev, Rajat M Gupta, Kasper Lage, Kristin G Ardlie, Joel N Hirschhorn, Eric S Lander, Jesse M Engreitz, Hilary K Finucane
Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases. Nature genetics (2023)
Ethan A G Baker, Denis Schapiro, Bianca Dumitrascu, Sanja Vickovic, Aviv Regev
In silico tissue generation and power analysis for spatial omics. Nature methods 20 (3) (2023)
Ethan A G Baker, Denis Schapiro, Bianca Dumitrascu, Sanja Vickovic, Aviv Regev
In silico tissue generation and power analysis for spatial omics. Nature methods 20 (3) (2023)
Ethan A G Baker, Denis Schapiro, Bianca Dumitrascu, Sanja Vickovic, Aviv Regev
In silico tissue generation and power analysis for spatial omics. Nature methods 20 (3) (2023)
Evgenij Fiskin, Gökçen Eraslan, Maria B Alora-Palli, Juan Manuel Leyva-Castillo, Sean Kim, Heather Choe, Caleb A Lareau, Helena Lau, Emily P Finan, Isabella Teixeira-Soldano, Brenna LaBere, Anne Chu, Brian Woods, Janet Chou, Michal Slyper, Julia Waldman, Sabina Islam, Lynda C Schneider, Wanda Phipatanakul, Craig Platt, Orit Rozenblatt-Rosen, Toni Marie Delorey, Jacques Deguine, Gideon P Smith, Raif S Geha, Aviv Regev, Ramnik J Xavier
Multi-modal skin atlas identifies a multicellular immune-stromal community associated with altered cornification and specific T cell expansion in atopic dermatitis. bioRxiv : the preprint server for biology (2023)
Florian V De Rop, Gert Hulselmans, Christopher Flerin, Paula Soler-Vila, Albert Rafels, Valerie Christiaens, Carmen Bravo González-Blas, Domenica Marchese, Ginevra Caratù, Suresh Poovathingal, Orit Rozenblatt-Rosen, Michael Slyper, Wendy Luo, Christoph Muus, Fabiana M Duarte, Rojesh Shrestha, S Tansu Bagdatli, M Ryan Corces, Lira Mamanova, Andrew Knights, Kerstin B Meyer, Ryan M Mulqueen, Akram Taherinasab, Patrick Maschmeyer, Joern Pezoldt, Camille Lucie Germaine Lambert, Marta Iglesias, Sebastián R Najle, Zain Y Dossani, Luciano G Martelotto, Zachary Daniel Burkett, Ronald Lebofsky, José Ignacio Martin-Subero, Satish Pillai, Arnau Sebé-Pedrós, Bart Deplancke, Sarah A Teichmann, Leif S Ludwig, Theodore P Braun, Andrew C Adey, William J Greenleaf, Jason D Buenrostro, Aviv Regev, Stein Aerts, Holger Heyn
Systematic benchmarking of single-cell ATAC-sequencing protocols. Nature biotechnology (2023)
Caleb A Lareau, Leif S Ludwig, Christoph Muus, Satyen H Gohil, Tongtong Zhao, Zachary Chiang, Karin Pelka, Jeffrey M Verboon, Wendy Luo, Elena Christian, Daniel Rosebrock, Gad A Getz, Genevieve M Boland, Fei Chen, Jason D Buenrostro, Nir Hacohen, Catherine J Wu, Martin J Aryee, Aviv Regev, Vijay G Sankaran
Author Correction: Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nature biotechnology (2023)
Methodios Ximerakis, Kristina M Holton, Richard M Giadone, Ceren Ozek, Monika Saxena, Samara Santiago, Xian Adiconis, Danielle Dionne, Lan Nguyen, Kavya M Shah, Jill M Goldstein, Caterina Gasperini, Ioannis A Gampierakis, Scott L Lipnick, Sean K Simmons, Sean M Buchanan, Amy J Wagers, Aviv Regev, Joshua Z Levin, Lee L Rubin
Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types. Nature aging 3 (3) (2023)
Simon Mages, Noa Moriel, Inbal Avraham-Davidi, Evan Murray, Jan Watter, Fei Chen, Orit Rozenblatt-Rosen, Johanna Klughammer, Aviv Regev, Mor Nitzan
TACCO unifies annotation transfer and decomposition of cell identities for single-cell and spatial omics. Nature biotechnology (2023)
Ethan A G Baker, Denis Schapiro, Bianca Dumitrascu, Sanja Vickovic, Aviv Regev
In silico tissue generation and power analysis for spatial omics. Nature methods 20 (3) (2023)
Johannes F Scheid, Basak Eraslan, Andrew Hudak, Eric M Brown, Dallis Sergio, Toni Marie Delorey, Devan Phillips, Ariel Lefkovith, Alison T Jess, Lennard W Duck, Charles O Elson, Hera Vlamakis, Damian Rafal Plichta, Jacques Deguine, Ashwin N Ananthakrishnan, Daniel B Graham, Aviv Regev, Ramnik J Xavier
Remodeling of colon plasma cell repertoire within ulcerative colitis patients. The Journal of experimental medicine 220 (4) (2023)
Methodios Ximerakis, Kristina M Holton, Richard M Giadone, Ceren Ozek, Monika Saxena, Samara Santiago, Xian Adiconis, Danielle Dionne, Lan Nguyen, Kavya M Shah, Jill M Goldstein, Caterina Gasperini, Ioannis A Gampierakis, Scott L Lipnick, Sean K Simmons, Sean M Buchanan, Amy J Wagers, Aviv Regev, Joshua Z Levin, Lee L Rubin
Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types. Nature aging 3 (3) (2023)
Methodios Ximerakis, Kristina M Holton, Richard M Giadone, Ceren Ozek, Monika Saxena, Samara Santiago, Xian Adiconis, Danielle Dionne, Lan Nguyen, Kavya M Shah, Jill M Goldstein, Caterina Gasperini, Ioannis A Gampierakis, Scott L Lipnick, Sean K Simmons, Sean M Buchanan, Amy J Wagers, Aviv Regev, Joshua Z Levin, Lee L Rubin
Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types. Nature aging 3 (3) (2023)
Lloyd Bod, Yoon-Chul Kye, Jingwen Shi, Elena Torlai Triglia, Alexandra Schnell, Johannes Fessler, Stephen M Ostrowski, Max Y Von-Franque, Juhi R Kuchroo, Rocky M Barilla, Sarah Zaghouani, Elena Christian, Toni Marie Delorey, Kanishka Mohib, Sheng Xiao, Nadine Slingerland, Christopher J Giuliano, Orr Ashenberg, Zhaorong Li, David M Rothstein, David E Fisher, Orit Rozenblatt-Rosen, Arlene H Sharpe, Francisco J Quintana, Lionel Apetoh, Aviv Regev, Vijay K Kuchroo
B-cell-specific checkpoint molecules that regulate anti-tumour immunity. Nature (2023)
Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, null null, Bonnie Berger, Dana Pe'er, Aviv Regev, Sarah A Teichmann, Francesca Finotello, F Alexander Wolf, Nir Yosef, Oliver Stegle, Fabian Joachim Theis
The scverse project provides a computational ecosystem for single-cell omics data analysis. Nature biotechnology (2023)
Johannes F Scheid, Basak Eraslan, Andrew Hudak, Eric M Brown, Dallis Sergio, Toni Marie Delorey, Devan Phillips, Ariel Lefkovith, Alison T Jess, Lennard W Duck, Charles O Elson, Hera Vlamakis, Damian Rafal Plichta, Jacques Deguine, Ashwin N Ananthakrishnan, Daniel B Graham, Aviv Regev, Ramnik J Xavier
Remodeling of colon plasma cell repertoire within ulcerative colitis patients. The Journal of experimental medicine 220 (4) (2023)
Davide Placido, Bo Yuan, Jessica X Hjaltelin, Chunlei Zheng, Amalie Dahl Haue, Piotr J Chmura, Chen Yuan, Jihye Kim, Renato Umeton, Gregory Antell, Alexander Chowdhury, Alexandra Franz, Lauren Brais, Elizabeth Andrews, Debora S Marks, Aviv Regev, Siamack Ayandeh, Mary T Brophy, Nhan V Do, Peter Kraft, Brian M Wolpin, Michael H Rosenthal, Nathanael R Fillmore, Soren Brunak, Chris Sander
A deep learning algorithm to predict risk of pancreatic cancer from disease trajectories. Nature medicine (2023)
Yunpeng Liu-Lupo, James Dongjoo Ham, Swarna K A Jeewajee, Lan Nguyen, Toni Marie Delorey, Azucena Ramos, David M Weinstock, Aviv Regev, Michael T Hemann
Integrated multi-omics analyses reveal homology-directed repair pathway as a unique dependency in near-haploid leukemia. Blood cancer journal 13 (1) (2023)
Ethan A G Baker, Denis Schapiro, Bianca Dumitrascu, Sanja Vickovic, Aviv Regev
In silico tissue generation and power analysis for spatial omics. Nature methods 20 (3) (2023)
Johannes F Scheid, Basak Eraslan, Andrew Hudak, Eric M Brown, Dallis Sergio, Toni Marie Delorey, Devan Phillips, Ariel Lefkovith, Alison T Jess, Lennard W Duck, Charles O Elson, Hera Vlamakis, Damian Rafal Plichta, Jacques Deguine, Ashwin N Ananthakrishnan, Daniel B Graham, Aviv Regev, Ramnik J Xavier
Remodeling of colon plasma cell repertoire within ulcerative colitis patients. The Journal of experimental medicine 220 (4) (2023)
Johannes F Scheid, Basak Eraslan, Andrew Hudak, Eric M Brown, Dallis Sergio, Toni Marie Delorey, Devan Phillips, Ariel Lefkovith, Alison T Jess, Lennard W Duck, Charles O Elson, Hera Vlamakis, Damian Rafal Plichta, Jacques Deguine, Ashwin N Ananthakrishnan, Daniel B Graham, Aviv Regev, Ramnik J Xavier
Remodeling of colon plasma cell repertoire within ulcerative colitis patients. The Journal of experimental medicine 220 (4) (2023)
Inbal Benhar, Jiarui Ding, Wenjun Yan, Irene E Whitney, Anne Jacobi, Malika Sud, Grace Burgin, Karthik Shekhar, Nicholas M Tran, Chen Wang, Zhigang He, Joshua R Sanes, Aviv Regev
Temporal single-cell atlas of non-neuronal retinal cells reveals dynamic, coordinated multicellular responses to central nervous system injury. Nature immunology (2023)
Livnat Jerby, Aviv Regev
DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data. Nature biotechnology 40 (10) (2022)
Ashish Noronha, Nishanth Belugali Nataraj, Joo Sang Lee, Benny Zhitomirsky, Yaara Oren, Sara Oster, Moshit Lindzen, Saptaparna Mukherjee, Rainer Will, Soma Ghosh, Arturo Simoni-Nieves, Aakanksha Verma, Rishita Chatterjee, Simone Borgoni, Welles Robinson, Sanju Sinha, Alexander Brandis, D Lucas Kerr, Wei Wu, Arunachalam Sekar, Suvendu Giri, Youngmin Chung, Diana Drago-Garcia, Brian P Danysh, Mattia Lauriola, Michelangelo Fiorentino, Andrea Ardizzoni, Moshe Oren, Collin M Blakely, Jideofor Ezike, Stefan Wiemann, Laxmi Parida, Trever G Bivona, Rami I Aqeilan, Joan S Brugge, Aviv Regev, Gad A Getz, Eytan Ruppin, Yosef Yarden
AXL and Error-Prone DNA Replication Confer Drug Resistance and Offer Strategies to Treat EGFR-Mutant Lung Cancer. Cancer discovery 12 (11) (2022)
Ruihan Tang, Nandini Acharya, Ayshwarya Subramanian, Vinee Purohit, Marcin Tabaka, Yu Hou, Danyang He, Karen Olivia Dixon, Connor Lambden, Junrong Xia, Orit Rozenblatt-Rosen, Raymond A Sobel, Chao Wang, Aviv Regev, Ana Carrizosa Anderson, Vijay K Kuchroo
Tim-3 adapter protein Bat3 acts as an endogenous regulator of tolerogenic dendritic cell function. Science immunology 7 (69) (2022)
William L Hwang, Karthik A Jagadeesh, Jimmy A Guo, Hannah I Hoffman, Payman Yadollahpour, Jason W Reeves, Rahul Mohan, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Orr Ashenberg, Samouil L Farhi, Denis Schapiro, Prajan Divakar, Eric M Miller, Daniel R Zollinger, George Eng, Jason M Schenkel, Jennifer Su, Carina Shiau, Patrick Yu, William A Freed-Pastor, Domenic Abbondanza, Arnav Mehta, Joshua Gould, Conner Lambden, Caroline B M Porter, Alexander Tsankov, Danielle Dionne, Julia Waldman, Michael S Cuoco, Lan Nguyen, Toni Marie Delorey, Devan Phillips, Jaimie L Barth, Marina Kem, Clifton Rodrigues, Debora Ciprani, Jorge Roldan, Piotr Zelga, Vjola Jorgji, Jonathan H Chen, Zackery Ely, Daniel Zhao, Kit Fuhrman, Robin Fropf, Joseph M Beechem, Jay S Loeffler, David P Ryan, Colin D Weekes, Cristina R Ferrone, Motaz Qadan, Martin J Aryee, Rakesh K Jain, Donna S Neuberg, Jennifer Y Wo, Theodore S Hong, Ramnik Xavier, Andrew J Aguirre, Orit Rozenblatt-Rosen, Mari A Mino-Kenudson, Carlos Fernandez-Del Castillo, Andrew S Liss, David Tsai Ting, Tyler Jacks, Aviv Regev
Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment. Nature genetics 54 (8) (2022)
Oana Ursu, James T Neal, Emily K Shea, Pratiksha I Thakore, Livnat Jerby, Lan Nguyen, Danielle Dionne, Celeste Diaz, Julia Bauman, Mariam Mounir Mosaad, Christian Fagre, April Lo, Maria McSharry, Andrew O Giacomelli, Seav Huong Ly, Orit Rozenblatt-Rosen, William C Hahn, Andrew J Aguirre, Alice H Berger, Aviv Regev, Jesse S Boehm
Massively parallel phenotyping of coding variants in cancer with Perturb-seq. Nature biotechnology 40 (6) (2022)
Gökçen Eraslan, Eugene Drokhlyansky, Shankara K Anand, Evgenij Fiskin, Ayshwarya Subramanian, Michal Slyper, Jiali Wang, Nicholas Van Wittenberghe, John M Rouhana, Julia Waldman, Orr Ashenberg, Monkol Lek, Danielle Dionne, Thet Su Win, Michael S Cuoco, Olena Kuksenko, Alexander M Tsankov, Philip A Branton, Jamie L Marshall, Anna Greka, Gad A Getz, Ayellet V Segrè, François Aguet, Orit Rozenblatt-Rosen, Kristin G Ardlie, Aviv Regev
Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function. Science (New York, N.Y.) 376 (6594) (2022)
Sanja Vickovic, Denis Schapiro, Konstantin Carlberg, Britta Lötstedt, Ludvig Larsson, Franziska Hildebrandt, Marina Korotkova, Aase H Hensvold, Anca I Catrina, Peter Karl Sorger, Vivianne Malmström, Aviv Regev, Patrik L Ståhl
Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium. Communications biology 5 (1) (2022)
Eeshit Dhaval Vaishnav, Carl G de Boer, Jennifer Molinet, Moran Yassour, Lin Fan, Xian Adiconis, Dawn A Thompson, Joshua Z Levin, Francisco A Cubillos, Aviv Regev
The evolution, evolvability and engineering of gene regulatory DNA. Nature 603 (7901) (2022)
Yun Zhang, Joana Liu Donaher, Sunny Das, Xin Li, Ferenc Reinhardt, Jordan A Krall, Arthur W Lambert, Prathapan Thiru, Heather R Keys, Mehreen Khan, Matan Hofree, Molly M Wilson, Ozlem Yedier-Bayram, Nathan A Lack, Tamer T Önder, Tugba Bagcı-Önder, Michael Tyler, Michael Mints, Aviv Regev, Jacqueline A Lees, Robert A Weinberg
Genome-wide CRISPR screen identifies PRC2 and KMT2D-COMPASS as regulators of distinct EMT trajectories that contribute differentially to metastasis. Nature cell biology 24 (4) (2022)
Yered H Pita-Juárez, Dimitra Karagkouni, Nikolaos Kalavros, Johannes C Melms, Sebastian Niezen, Toni M Delorey, Adam L Essene, Olga R Brook, Deepti Pant, Disha Skelton-Badlani, Pourya Naderi Yeganeh, Pinzhu Huang, Liuliu Pan, Tyler Hether, Tallulah S Andrews, Carly G K Ziegler, Jason Reeves, Andriy Myloserdnyy, Rachel Chen, Andy Nam, Stefan Phelan, Yan Liang, Amit Dipak Amin, Jana Biermann, Hanina Hibshoosh, Molly Veregge, Zachary Kramer, Christopher Jacobs, Yusuf Yalcin, Devan Phillips, Michal Slyper, Ayshwarya Subramanian, Orr Ashenberg, Zohar Bloom-Ackermann, Victoria M Tran, James Gomez, Alexander Sturm, Shuting Zhang, Stephen J Fleming, Sarah Warren, Joseph Beechem, Deborah Hung, Mehrtash Babadi, Robert F Padera, Sonya A MacParland, Gary D Bader, Nasser Imad, Isaac H Solomon, Eric Miller, Stefan Riedel, Caroline B M Porter, Alexandra-Chloé Villani, Linus T-Y Tsai, Winston A Hide, Gyongyi Szabo, Jonathan Hecht, Orit Rozenblatt-Rosen, Alex K Shalek, Benjamin Izar, Aviv Regev, Yury V Popov, Z Gordon Jiang, Ioannis S Vlachos
A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients. bioRxiv : the preprint server for biology (2022)
Rebecca C Larson, Michael C Kann, Stefanie R Bailey, Nicholas J Haradhvala, Paula Montero Llopis, Amanda A Bouffard, Irene Scarfó, Mark B Leick, Korneel Grauwet, Trisha R Berger, Kai Stewart, Praju Vikas Anekal, Max Jan, Julia Joung, Andrea Schmidts, Tamara Ouspenskaia, Travis Law, Aviv Regev, Gad Getz, Marcela V Maus
CAR T cell killing requires the IFNγR pathway in solid but not liquid tumours. Nature 604 (7906) (2022)
Sanja Vickovic, B Lötstedt, Johanna Klughammer, S Mages, Å Segerstolpe, Orit Rozenblatt-Rosen, Aviv Regev
SM-Omics is an automated platform for high-throughput spatial multi-omics. Nature communications 13 (1) (2022)
Richard K Perez, M Grace Gordon, Meena Subramaniam, Min Cheol Kim, George C Hartoularos, Sasha Targ, Yang Sun, Anton Ogorodnikov, Raymund Bueno, Andrew Lu, Mike Thompson, Nadav Rappoport, Andrew W Dahl, Cristina M Lanata, Mehrdad Matloubian, Lenka Maliskova, Serena S Kwek, Tony Li, Michal Slyper, Julia Waldman, Danielle Dionne, Orit Rozenblatt-Rosen, Lawrence Fong, Maria Dall'Era, Brunilda Balliu, Aviv Regev, Rebecca Grainger, Lindsey A Criswell, Noah A Zaitlen, Chun Jimmie Ye
Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus. Science (New York, N.Y.) 376 (6589) (2022)
Karthik A Jagadeesh, Kushal K Dey, Daniel T Montoro, Rahul Mohan, Steven Gazal, Jesse M Engreitz, Ramnik J Xavier, Alkes L Price, Aviv Regev
Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics. Nature genetics 54 (10) (2022)
Eran Hodis, Elena Torlai Triglia, John Y H Kwon, Tommaso Biancalani, Labib R Zakka, Saurabh Parkar, Jan-Christian Hütter, Lorenzo Buffoni, Toni Marie Delorey, Devan Phillips, Danielle Dionne, Lan T Nguyen, Denis Schapiro, Zoltan Maliga, Connor A Jacobson, Ayal Hendel, Orit Rozenblatt-Rosen, Martin C Mihm, Levi A Garraway, Aviv Regev
Stepwise-edited, human melanoma models reveal mutations' effect on tumor and microenvironment. Science (New York, N.Y.) 376 (6592) (2022)
Giovanni Palla, David S Fischer, Aviv Regev, Fabian Joachim Theis
Spatial components of molecular tissue biology. Nature biotechnology 40 (3) (2022)
Jennifer E Rood, Aidan Maartens, Anna Hupalowska, Sarah A Teichmann, Aviv Regev
Impact of the Human Cell Atlas on medicine. Nature medicine (2022)
Denis Schapiro, Artem Sokolov, Clarence Yapp, Yu-An Chen, Jeremy L Muhlich, Joshua Hess, Allison L Creason, Ajit J Nirmal, Gregory J Baker, Maulik K Nariya, Jia-Ren Lin, Zoltan Maliga, Connor A Jacobson, Matthew W Hodgman, Juha Ruokonen, Samouil L Farhi, Domenic Abbondanza, Eliot T McKinley, Daniel Persson, Courtney Betts, Shamilene Sivagnanam, Aviv Regev, Jeremy Goecks, D Borden Lacy, Lisa M Coussens, Sandro Santagata, Peter Karl Sorger
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nature methods (2021)
Orit Rozenblatt-Rosen, Jay W Shin, Jennifer E Rood, Anna Hupalowska, null null, Aviv Regev, Holger Heyn
Building a high-quality Human Cell Atlas. Nature biotechnology 39 (2) (2021)
Yaara Oren, Michael Tsabar, Michael S Cuoco, Liat Amir-Zilberstein, Heidie F Cabanos, Jan-Christian Hütter, Bomiao Hu, Pratiksha I Thakore, Marcin Tabaka, Charles P Fulco, William N Colgan, Brandon M Cuevas, Sara A Hurvitz, Dennis J Slamon, Amy Deik, Kerry A Pierce, Andrew T Chan, Aaron N Hata, Elma Zaganjor, Galit Lahav, Katerina Politi, Joan S Brugge, Aviv Regev
Cycling cancer persister cells arise from lineages with distinct programs. Nature 596 (7873) (2021)
Ronan Chaligné, Federico Gaiti, Dana Silverbush, Joshua S Schiffman, Hannah R Weisman, Lloyd Kluegel, Simon Gritsch, Sunil D Deochand, L Nicolas Gonzalez Castro, Alyssa R Richman, Johanna Klughammer, Tommaso Biancalani, Christoph Muus, Caroline Sheridan, Alicia Alonso, Franco Izzo, Jane Park, Orit Rozenblatt-Rosen, Aviv Regev, Mario L Suvà, Dan A Landau
Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states. Nature genetics 53 (10) (2021)
Mahesh Raundhal, Shrestha Ghosh, Samuel A Myers, Michael S Cuoco, Meromit Singer, Steven A Carr, Sushrut S Waikar, Joseph V Bonventre, Jerome Ritz, Richard M Stone, David P Steensma, Aviv Regev, Laurie H Glimcher
Blockade of IL-22 signaling reverses erythroid dysfunction in stress-induced anemias. Nature immunology 22 (4) (2021)
Zuri A Sullivan, William Khoury-Hanold, Jaechul Lim, Chris Smillie, Moshe Biton, Bernardo S Reis, Rachel K Zwick, Scott D Pope, Kavita Israni-Winger, Roham Parsa, Naomi H Philip, Saleh Rashed, Noah W Palm, Andrew Wang, Daniel Mucida, Aviv Regev, Ruslan Medzhitov
γδ T cells regulate the intestinal response to nutrient sensing. Science (New York, N.Y.) 371 (6535) (2021)
Evgenij Fiskin, Caleb A Lareau, Leif S Ludwig, Gökçen Eraslan, Feimei Liu, Aaron M Ring, Ramnik J Xavier, Aviv Regev
Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC. Nature biotechnology (2021)
Emilie Crouchet, Simonetta Bandiera, Naoto Fujiwara, Shen Li, Hussein El Saghire, Mirian Fernández-Vaquero, Tobias Riedl, Xiaochen Sun, Hadassa Hirschfield, Frank Jühling, Shijia Zhu, Natascha Roehlen, Clara Ponsolles, Laura Heydmann, Antonio Saviano, Tongqi Qian, Anu Venkatesh, Joachim Lupberger, Thomas F Baumert, Mozhdeh Sojoodi, Marine A Oudot, François H T Duong, Ricard Masia, Lan Wei, Christine Thumann, Sarah C Durand, Victor González-Motos, Danijela Heide, Jenny Hetzer, Shigeki Nakagawa, Atsushi Ono, Won-Min Song, Takaaki Higashi, Roberto Sanchez, Rosa S Kim, C Billie Bian, Karun Kiani, Tom Croonenborghs, Aravind Subramanian, Raymond T Chung, Beate K Straub, Detlef Schuppan, Maliki Ankavay, Laurence Cocquerel, Evelyne Schaeffer, Nicolas Goossens, Anna P Koh, Milind Mahajan, Venugopalan D Nair, Ganesh Gunasekaran, Myron E Schwartz, Nabeel El-Bardeesy, Alex K Shalek, Orit Rozenblatt-Rosen, Aviv Regev, Emanuele Felli, Patrick Pessaux, Kenneth K Tanabe, Mathias F Heikenwälder, Catherine Schuster, Nathalie Pochet, Mirjam B Zeisel, Bryan C Fuchs, Yujin Hoshida, Thomas F Baumert
A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery. Nature communications 12 (1) (2021)
Tamara Ouspenskaia, Travis Law, Karl R Clauser, Susan Klaeger, Siranush Sarkizova, François Aguet, Bo Li, Elena Christian, Binyamin Asher Knisbacher, Phuong M Le, Christina R Hartigan, Hasmik Keshishian, Annie Apffel, Giacomo Oliveira, Wandi Zhang, Sarah Chen, Yuen Ting Chow, Zhe Ji, Irwin Jungreis, Sachet A Shukla, Sune Justesen, Pavan Bachireddy, Manolis Kellis, Gad A Getz, Nir Hacohen, Derin B Keskin, Steven A Carr, Catherine J Wu, Aviv Regev
Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nature biotechnology (2021)
Eleni P Mimitou, Caleb A Lareau, Kelvin Y Chen, Andre L Zorzetto-Fernandes, Yuhan Hao, Yusuke Takeshima, Wendy Luo, Tse-Shun Huang, Bertrand Z Yeung, Efthymia Papalexi, Pratiksha I Thakore, Tatsuya Kibayashi, James Badger Wing, Mayu Hata, Rahul Satija, Kristopher L Nazor, Shimon Sakaguchi, Leif S Ludwig, Vijay G Sankaran, Aviv Regev, Peter Smibert
Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nature biotechnology 39 (10) (2021)
Trygve E Bakken, Nikolas L Jorstad, Qiwen Hu, Blue B Lake, Wei Tian, Brian E Kalmbach, Megan Crow, Rebecca D Hodge, Fenna M Krienen, Staci A Sorensen, Jeroen Eggermont, Zizhen Yao, Brian D Aevermann, Andrew I Aldridge, Anna Bartlett, Darren Bertagnolli, Tamara Casper, Rosa G Castanon, Kirsten Crichton, Tanya L Daigle, Rachel Dalley, Nick Dee, Nikolai C Dembrow, Dinh Diep, Song-Lin Ding, Weixiu Dong, Rongxin Fang, Stephan Fischer, Melissa Goldman, Jeff Goldy, Lucas T Gray, Brian R Herb, Xiaomeng Hou, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Baldur van Lew, Yang Eric Li, Christine S Liu, Hanqing Liu, Jacinta D Lucero, Anup A Mahurkar, Delissa McMillen, Jeremy A Miller, Marmar Moussa, Joseph R Nery, Philip R Nicovich, Sheng-Yong Niu, Joshua Orvis, Julia K Osteen, Scott Owen, Carter R Palmer, Trangthanh H Pham, Nongluk Plongthongkum, Olivier Poirion, Nora M Reed, Christine Rimorin, Angeline Rivkin, William J Romanow, Adriana E Sedeño-Cortés, Kimberly Siletti, Saroja Somasundaram, Josef Sulc, Michael Tieu, Amy Torkelson, Herman Tung, Xinxin Wang, Fangming Xie, Anna Marie Yanny, Renee Zhang, Seth A Ament, M Margarita Behrens, Hector Corrada Bravo, Jerold Chun, Alexander Dobin, Jesse Gillis, Ronna Hertzano, Patrick R Hof, Thomas Höllt, Gregory D Horwitz, C Dirk Keene, Peter V Kharchenko, Andrew L Ko, Boudewijn P F Lelieveldt, Chongyuan Luo, Eran A Mukamel, António Pinto-Duarte, Sebastian Preissl, Aviv Regev, Bing Ren, Richard H Scheuermann, Kimberly A Smith, William J Spain, Owen R White, Christof Koch, Michael J Hawrylycz, Bosiljka Tasic, Evan Z Macosko, Steven A McCarroll, Jonathan T Ting, Hongkui Zeng, Kun Zhang, Guoping Feng, Joseph R Ecker, Sten Linnarsson, Ed S Lein
Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature 598 (7879) (2021)
Toni Marie Delorey, Carly G K Ziegler, Graham Heimberg, Rachelly Normand, Yiming Yang, Åsa Segerstolpe, Domenic Abbondanza, Stephen J Fleming, Ayshwarya Subramanian, Daniel T Montoro, Karthik A Jagadeesh, Kushal K Dey, Pritha Sen, Michal Slyper, Yered H Pita-Juárez, Devan Phillips, Jana Biermann, Zohar Bloom-Ackermann, Nikolaos Barkas, Andrea Ganna, James Gomez, Johannes C Melms, Igor Katsyv, Erica Normandin, Pourya Naderi, Yury V Popov, Siddharth S Raju, Sebastian Niezen, Linus T-Y Tsai, Katherine J Siddle, Malika Sud, Victoria M Tran, Shamsudheen K Vellarikkal, Yiping Wang, Liat Amir-Zilberstein, Deepak S Atri, Joseph Beechem, Olga R Brook, Jonathan Chen, Prajan Divakar, Phylicia Dorceus, Jesse M Engreitz, Adam Essene, Donna M Fitzgerald, Robin Fropf, Steven Gazal, Joshua Gould, John Grzyb, Tyler Harvey, Jonathan Hecht, Tyler Hether, Judit Jané-Valbuena, Michael Leney-Greene, Hui Ma, Cristin McCabe, Daniel E McLoughlin, Eric M Miller, Christoph Muus, Mari Niemi, Robert Padera, Liuliu Pan, Deepti Pant, Carmel Pe'er, Jenna Pfiffner-Borges, Christopher J Pinto, Jacob Plaisted, Jason Reeves, Marty Ross, Melissa Rudy, Erroll H Rueckert, Michelle Siciliano, Alexander Sturm, Ellen Todres, Avinash Waghray, Sarah Warren, Shuting Zhang, Daniel R Zollinger, Lisa Cosimi, Rajat M Gupta, Nir Hacohen, Hanina Hibshoosh, Winston Hide, Alkes L Price, Jayaraj Rajagopal, Purushothama Rao Tata, Stefan Riedel, Gyongyi Szabo, Timothy L Tickle, Patrick T Ellinor, Deborah Hung, Pardis C Sabeti, Richard Novak, Robert Rogers, Donald E Ingber, Z Gordon Jiang, Dejan Juric, Mehrtash Babadi, Samouil L Farhi, Benjamin Izar, James R Stone, Ioannis S Vlachos, Isaac H Solomon, Orr Ashenberg, Caroline B M Porter, Bo Li, Alex K Shalek, Alexandra-Chloé Villani, Orit Rozenblatt-Rosen, Aviv Regev
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature 595 (7865) (2021)
Tommaso Biancalani, Gabriele Scalia, Lorenzo Buffoni, Raghav Avasthi, Ziqing Lu, Aman Sanger, Neriman Tokcan, Charles R Vanderburg, Åsa Segerstolpe, Meng Zhang, Inbal Avraham-Davidi, Sanja Vickovic, Mor Nitzan, Sai Ma, Ayshwarya Subramanian, Michal Lipinski, Jason Buenrostro, Nik Bear Brown, Duccio Fanelli, Xiaowei Zhuang, Evan Z Macosko, Aviv Regev
Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. Nature methods 18 (11) (2021)
Velina Kozareva, Caroline Martin, Tomas Osorno, Stephanie Rudolph, Chong Guo, Charles Vanderburg, Naeem Nadaf, Aviv Regev, Wade G Regehr, Evan Z Macosko
A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types. Nature 598 (7879) (2021)
Xin Jin, Sean K Simmons, Amy Guo, Ashwin S Shetty, Michelle Ko, Lan Nguyen, Vahbiz Jokhi, Elise Robinson, Paul Oyler, Nathan Curry, Giulio Deangeli, Simona Lodato, Joshua Z Levin, Aviv Regev, Feng Zhang, Paola Arlotta
In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes. Science (New York, N.Y.) 370 (6520) (2021)
Zizhen Yao, Hanqing Liu, Fangming Xie, Stephan Fischer, Ricky S Adkins, Andrew I Aldridge, Seth A Ament, Anna Bartlett, M Margarita Behrens, Koen Van den Berge, Darren Bertagnolli, Hector Roux de Bezieux, Tommaso Biancalani, Ali Sina Booeshaghi, Héctor Corrada Bravo, Tamara Casper, Carlo Colantuoni, Jonathan Crabtree, Heather H Creasy, Kirsten Crichton, Megan Crow, Nick Dee, Elizabeth L Dougherty, Wayne I Doyle, Sandrine Dudoit, Rongxin Fang, Victor Felix, Olivia Fong, Michelle G Giglio, Jeff Goldy, Michael J Hawrylycz, Brian R Herb, Ronna Hertzano, Xiaomeng Hou, Qiwen Hu, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Yang Eric Li, Jacinta D Lucero, Chongyuan Luo, Anup A Mahurkar, Delissa McMillen, Naeem M Nadaf, Joseph R Nery, Thuc Nghi Nguyen, Sheng-Yong Niu, Vasilis Ntranos, Joshua Orvis, Julia K Osteen, Trangthanh H Pham, António Pinto-Duarte, Olivier Poirion, Sebastian Preissl, Elizabeth Purdom, Christine Rimorin, Davide Risso, Angeline C Rivkin, Kimberly A Smith, Kelly Street, Josef Sulc, Valentine Svensson, Michael Tieu, Amy Torkelson, Herman Tung, Eeshit Dhaval Vaishnav, Charles R Vanderburg, Cindy T J van Velthoven, Xinxin Wang, Owen R White, Z Josh Huang, Peter V Kharchenko, Lior Pachter, John Ngai, Aviv Regev, Bosiljka Tasic, Joshua D Welch, Jesse Gillis, Evan Z Macosko, Bing Ren, Joseph R Ecker, Hongkui Zeng, Eran A Mukamel
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature 598 (7879) (2021)
Shahar Alon, Daniel R Goodwin, Anubhav Sinha, Asmamaw T Wassie, Fei Chen, Evan R Daugharthy, Yosuke Bando, Atsushi Kajita, Andrew G Xue, Karl Marrett, Robert Prior, Yi Cui, Andrew C Payne, Chun-Chen Yao, Ho-Jun Suk, Ru Wang, Chih-Chieh Jay Yu, Paul W Tillberg, Paul L Reginato, Nikita Pak, Songlei Liu, Sukanya Punthambaker, Eswar P R Iyer, Richie E Kohman, Jeremy A Miller, Ed S Lein, Ana Lako, Nicole Cullen, Scott Rodig, Karla Helvie, Daniel L Abravanel, Nikhil Wagle, Bruce E Johnson, Johanna Klughammer, Michal Slyper, Julia Waldman, Judit Jané-Valbuena, Orit Rozenblatt-Rosen, Aviv Regev, null null, George M Church, Adam H Marblestone, Edward S Boyden
Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. Science (New York, N.Y.) 371 (6528) (2021)
Brian Cleary, Brooke Simonton, Jon Bezney, Evan Murray, Shahul Alam, Anubhav Sinha, Ehsan Habibi, Jamie L Marshall, Eric S Lander, Fei Chen, Aviv Regev
Compressed sensing for highly efficient imaging transcriptomics. Nature biotechnology 39 (8) (2021)
Chris J Frangieh, Johannes C Melms, Pratiksha I Thakore, Kathryn R Geiger-Schuller, Patricia Ho, Adrienne M Luoma, Brian Cleary, Livnat Jerby, Shruti Malu, Michael S Cuoco, Maryann Zhao, Casey R Ager, Meri Rogava, Lila Hovey, Asaf Rotem, Chantale Bernatchez, Kai W Wucherpfennig, Bruce E Johnson, Orit Rozenblatt-Rosen, Dirk Schadendorf, Aviv Regev, Benjamin Izar
Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion. Nature genetics 53 (3) (2021)
Karen Olivia Dixon, Marcin Tabaka, Markus A Schramm, Sheng Xiao, Ruihan Tang, Danielle Dionne, Ana Carrizosa Anderson, Orit Rozenblatt-Rosen, Aviv Regev, Vijay K Kuchroo
TIM-3 restrains anti-tumour immunity by regulating inflammasome activation. Nature 595 (7865) (2021)
Livnat Jerby, Cyril Neftel, Marni E Shore, Hannah R Weisman, Nathan D Mathewson, Matthew J McBride, Brian Haas, Benjamin Izar, Angela Volorio, Gaylor Boulay, Luisa Cironi, Alyssa R Richman, Liliane C Broye, Joseph M Gurski, Christina C Luo, Ravindra Mylvaganam, Lan Nguyen, Shaolin Mei, Johannes C Melms, Christophe Georgescu, Ofir Cohen, Jorge E Buendia-Buendia, Asa Segerstolpe, Malika Sud, Michael S Cuoco, Danny Labes, Simon Gritsch, Daniel R Zollinger, Nicole Ortogero, Joseph M Beechem, G Petur Nielsen, Ivan Chebib, Tu Nguyen-Ngoc, Michael Montemurro, Gregory M Cote, Edwin Choy, Igor Letovanec, Stephane Cherix, Nikhil Wagle, Peter Karl Sorger, Alex B Haynes, John T Mullen, Ivan Stamenkovic, Miguel N Rivera, Cigall Kadoch, Kai W Wucherpfennig, Orit Rozenblatt-Rosen, Mario L Suvà, Nicolò Riggi, Aviv Regev
Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma. Nature medicine 27 (2) (2021)

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Aviv Regev (A Regev)