Martin J Aryee (Martin Aryee)

ORCID

Publication Activity (10 Years)

Years Active: 2014-2024
Publications (10 Years): 35

Top Venues

Nature biotechnology

Nature methods

Nature communications

Nature immunology

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

Publications

Jonathan H Chen, Linda T Nieman, Maxwell Spurrell, Vjola Jorgji, Liad Elmelech, Peter Richieri, Katherine H Xu, Roopa Madhu, Milan Parikh, Izabella Zamora, Arnav Mehta, Christopher S Nabel, Samuel S Freeman, Joshua D Pirl, Chenyue Lu, Catherine B Meador, Jaimie L Barth, Mustafa Sakhi, Alexander L Tang, Siranush Sarkizova, Colles Price, Nicolas F Fernandez, George Emanuel, Jiang He, Katrina Van Raay, Jason W Reeves, Keren Yizhak, Matan Hofree, Angela R Shih, Moshe Sade-Feldman, Genevieve Marie Boland, Karin Pelka, Martin J Aryee, Mari A Mino-Kenudson, Justin F Gainor, Ilya Korsunsky, Nir Hacohen
Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy. Nature immunology (2024)
Jonathan H Chen, Linda T Nieman, Maxwell Spurrell, Vjola Jorgji, Liad Elmelech, Peter Richieri, Katherine H Xu, Roopa Madhu, Milan Parikh, Izabella Zamora, Arnav Mehta, Christopher S Nabel, Samuel S Freeman, Joshua D Pirl, Chenyue Lu, Catherine B Meador, Jaimie L Barth, Mustafa Sakhi, Alexander L Tang, Siranush Sarkizova, Colles Price, Nicolas F Fernandez, George Emanuel, Jiang He, Katrina Van Raay, Jason W Reeves, Keren Yizhak, Matan Hofree, Angela R Shih, Moshe Sade-Feldman, Genevieve Marie Boland, Karin Pelka, Martin J Aryee, Mari A Mino-Kenudson, Justin F Gainor, Ilya Korsunsky, Nir Hacohen
Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy. Nature immunology 25 (4) (2024)
Jonathan H Chen, Linda T Nieman, Maxwell Spurrell, Vjola Jorgji, Liad Elmelech, Peter Richieri, Katherine H Xu, Roopa Madhu, Milan Parikh, Izabella Zamora, Arnav Mehta, Christopher S Nabel, Samuel S Freeman, Joshua D Pirl, Chenyue Lu, Catherine B Meador, Jaimie L Barth, Mustafa Sakhi, Alexander L Tang, Siranush Sarkizova, Colles Price, Nicolas F Fernandez, George Emanuel, Jiang He, Katrina Van Raay, Jason W Reeves, Keren Yizhak, Matan Hofree, Angela R Shih, Moshe Sade-Feldman, Genevieve Marie Boland, Karin Pelka, Martin J Aryee, Mari A Mino-Kenudson, Justin F Gainor, Ilya Korsunsky, Nir Hacohen
Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy. Nature immunology 25 (4) (2024)
Jonathan H Chen, Linda T Nieman, Maxwell Spurrell, Vjola Jorgji, Liad Elmelech, Peter Richieri, Katherine H Xu, Roopa Madhu, Milan Parikh, Izabella Zamora, Arnav Mehta, Christopher S Nabel, Samuel S Freeman, Joshua D Pirl, Chenyue Lu, Catherine B Meador, Jaimie L Barth, Mustafa Sakhi, Alexander L Tang, Siranush Sarkizova, Colles Price, Nicolas F Fernandez, George Emanuel, Jiang He, Katrina Van Raay, Jason W Reeves, Keren Yizhak, Matan Hofree, Angela R Shih, Moshe Sade-Feldman, Genevieve Marie Boland, Karin Pelka, Martin J Aryee, Mari A Mino-Kenudson, Justin F Gainor, Ilya Korsunsky, Nir Hacohen
Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy. Nature immunology 25 (4) (2024)
Corriene E Sept, Y Esther Tak, Christian G Cerda-Smith, Haley M Hutchinson, Viraat Goel, Marco Blanchette, Mital S Bhakta, Anders S Hansen, J Keith Joung, Sarah Johnstone, Christine E Eyler, Martin J Aryee
High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion dynamics. bioRxiv : the preprint server for biology (2023)
Rajendran Sanalkumar, Rui Dong, Lukuo Lee, Yu-Hang Xing, Sowmya Iyer, Igor Letovanec, Stefano La Rosa, Giovanna Finzi, Elettra Musolino, Roberto Papait, Ivan A Chebib, G Petur Nielsen, Raffaele Renella, Gregory M Cote, Edwin Choy, Martin J Aryee, Kimberly Stegmaier, Ivan Stamenkovic, Miguel N Rivera, Nicolò Riggi
Highly connected 3D chromatin networks established by an oncogenic fusion protein shape tumor cell identity. Science advances 9 (13) (2023)
Avril K Coley, Chenyue Lu, Amaya Pankaj, Matthew J Emmett, Evan R Lang, Yuhui Song, Katherine H Xu, Nova Xu, Bidish K Patel, Abhijit Chougule, Linda T Nieman, Martin J Aryee, Cristina R Ferrone, Vikram Deshpande, Joseph W Franses, David T Ting
Dysregulated Repeat Element Viral-like Immune Response in Hepatocellular Carcinoma. bioRxiv : the preprint server for biology (2023)
Rajendran Sanalkumar, Rui Dong, Lukuo Lee, Yu-Hang Xing, Sowmya Iyer, Igor Letovanec, Stefano La Rosa, Giovanna Finzi, Elettra Musolino, Roberto Papait, Ivan A Chebib, G Petur Nielsen, Raffaele Renella, Gregory M Cote, Edwin Choy, Martin J Aryee, Kimberly Stegmaier, Ivan Stamenkovic, Miguel N Rivera, Nicolò Riggi
Highly connected 3D chromatin networks established by an oncogenic fusion protein shape tumor cell identity. Science advances 9 (13) (2023)
Avril K Coley, Chenyue Lu, Amaya Pankaj, Matthew J Emmett, Evan R Lang, Yuhui Song, Katherine H Xu, Nova Xu, Bidish K Patel, Abhijit Chougule, Linda T Nieman, Martin J Aryee, Cristina R Ferrone, Vikram Deshpande, Joseph W Franses, David T Ting
Dysregulated Repeat Element Viral-like Immune Response in Hepatocellular Carcinoma. bioRxiv : the preprint server for biology (2023)
Emely Möller, Viviane Praz, Sanalkumar Rajendran, Rui Dong, Alexandra Cauderay, Yu-Hang Xing, Lukuo Lee, Carlo Fusco, Liliane C Broye, Luisa Cironi, Sowmya Iyer, Shruthi Rengarajan, Mary E Awad, Beverly Naigles, Igor Letovanec, Nicola Ormas, Giovanna Finzi, Stefano La Rosa, Fausto Sessa, Ivan Chebib, G Petur Nielsen, Antonia Digklia, Dimitrios Spentzos, Gregory M Cote, Edwin Choy, Martin J Aryee, Ivan Stamenkovic, Gaylor Boulay, Miguel N Rivera, Nicolò Riggi
EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in Clear Cell Sarcoma. Nature communications 13 (1) (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)
Christopher B Lietz, Erik T Newman, Andrew D Kelly, David H Xiang, Ziying Zhang, Caroline A Luscko, Santiago A Lozano-Calderon, David H Ebb, Kevin A Raskin, Gregory M Cote, Edwin Choy, G Petur Nielsen, Benjamin Haibe-Kains, Martin J Aryee, Dimitrios Spentzos
Genome-wide DNA methylation patterns reveal clinically relevant predictive and prognostic subtypes in human osteosarcoma. Communications biology 5 (1) (2022)
Leif S Ludwig, Caleb A Lareau, Erik L Bao, Nan Liu, Taiju Utsugisawa, Alex M Tseng, Samuel A Myers, Jeffrey M Verboon, Jacob C Ulirsch, Wendy Luo, Christoph Muus, Claudia Fiorini, Meagan E Olive, Christopher M Vockley, Mathias Munschauer, Abigail Hunter, Hiromi Ogura, Toshiyuki Yamamoto, Hiroko Inada, Shinichiro Nakagawa, Shuichi Ozono, Vidya Subramanian, Roberto Chiarle, Bertil Glader, Steven A Carr, Martin J Aryee, Anshul Kundaje, Stuart H Orkin, Aviv Regev, Timothy L McCavit, Hitoshi Kanno, Vijay G Sankaran
Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1. Blood 139 (16) (2022)
Mihir Rajurkar, Aparna R Parikh, Alexander Solovyov, Eunae You, Anupriya S Kulkarni, Chong Chu, Katherine H Xu, Christopher Jaicks, Martin S Taylor, Connie Wu, Katherine A Alexander, Charly R Good, Annamaria Szabolcs, Stefanie Gerstberger, Antuan V Tran, Nova Xu, Richard Y Ebright, Emily E Van Seventer, Kevin D Vo, Eric C Tai, Chenyue Lu, Jasmin Joseph-Chazan, Michael J Raabe, Linda T Nieman, Niyati Desai, Kshitij S Arora, Matteo Ligorio, Vishal Thapar, Limor Cohen, Padric M Garden, Yasmeen Senussi, Hui Zheng, Jill N Allen, Lawrence S Blaszkowsky, Jeffrey W Clark, Lipika Goyal, Jennifer Y Wo, David P Ryan, Ryan B Corcoran, Vikram Deshpande, Miguel N Rivera, Martin J Aryee, Theodore S Hong, Shelley L Berger, David R Walt, Kathleen H Burns, Peter J Park, Benjamin D Greenbaum, David Tsai Ting
Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer. Cancer discovery 12 (6) (2022)
Tjada A Schult, Mara J Lauer, Yannick Berker, Marcella Regina Cardoso, Lindsey A Vandergrift, Piet Habbel, Johannes Nowak, Matthias Taupitz, Martin J Aryee, Mari A Mino-Kenudson, David Chistopher Christiani, Leo L Cheng
Screening human lung cancer with predictive models of serum magnetic resonance spectroscopy metabolomics. Proceedings of the National Academy of Sciences of the United States of America 118 (51) (2022)
Hongcang Gu, Ayush T Raman, Xiaoxue Wang, Federico Gaiti, Ronan Chaligné, Arman W Mohammad, Aleksandra Arczewska, Zachary D Smith, Dan A Landau, Martin J Aryee, Alexander Meissner, Andreas Gnirke
Smart-RRBS for single-cell methylome and transcriptome analysis. Nature protocols 16 (8) (2021)
Nikolay L Malinin, GaHyun Lee, Cicera R Lazzarotto, Yichao Li, Zongli Zheng, Nhu T Nguyen, Matthew Liebers, Ved V Topkar, A John Iafrate, Long P Le, Martin J Aryee, J Keith Joung, Shengdar Q Tsai
Defining genome-wide CRISPR-Cas genome-editing nuclease activity with GUIDE-seq. Nature protocols 16 (12) (2021)
Y Esther Tak, Joy E Horng, Nicholas T Perry, Hayley T Schultz, Sowmya Iyer, Qiuming Yao, Luli S Zou, Martin J Aryee, Luca Pinello, J Keith Joung
Augmenting and directing long-range CRISPR-mediated activation in human cells. Nature methods 18 (9) (2021)
Sarah J Shareef, Samantha M Bevill, Ayush T Raman, Martin J Aryee, Peter van Galen, Volker Hovestadt, Bradley E Bernstein
Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells. Nature biotechnology 39 (9) (2021)
Julian Grünewald, Ronghao Zhou, Caleb A Lareau, Sara P Garcia, Sowmya Iyer, Bret R Miller, Lukas M Langner, Jonathan Y Hsu, Martin J Aryee, J Keith Joung
A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing. Nature biotechnology 38 (7) (2020)
Caleb A Lareau, Fabiana M Duarte, Jennifer G Chew, Vinay K Kartha, Zachary Daniel Burkett, Andrew S Kohlway, Dmitry Pokholok, Martin J Aryee, Frank J Steemers, Ronald Lebofsky, Jason D Buenrostro
Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility. Nature biotechnology 37 (8) (2019)
Yannick Berker, Lindsey A Vandergrift, Isabel Wagner, Li Su, Johannes Kurth, Andreas Schuler, Sarah S Dinges, Piet Habbel, Johannes Nowak, Eugene Mark, Martin J Aryee, David C Christiani, Leo L Cheng
Magnetic Resonance Spectroscopy-based Metabolomic Biomarkers for Typing, Staging, and Survival Estimation of Early-Stage Human Lung Cancer. Scientific reports 9 (1) (2019)
Jacob C Ulirsch, Caleb A Lareau, Erik L Bao, Leif S Ludwig, Michael H Guo, Christian Benner, Ansuman T Satpathy, Vinay K Kartha, Rany M Salem, Joel N Hirschhorn, Hilary K Finucane, Martin J Aryee, Jason D Buenrostro, Vijay G Sankaran
Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nature genetics 51 (4) (2019)
Julian Grünewald, Ronghao Zhou, Sowmya Iyer, Caleb A Lareau, Sara P Garcia, Martin J Aryee, J Keith Joung
CRISPR DNA base editors with reduced RNA off-target and self-editing activities. Nature biotechnology 37 (9) (2019)
Killian S Hanlon, Benjamin P Kleinstiver, Sara P Garcia, Mikołaj Piotr Zaborowski, Adrienn Volak, Stefan E Spirig, Alissa Muller, Alexander A Sousa, Shengdar Q Tsai, Niclas E Bengtsson, Camilla Lööv, Martin Ingelsson, Jeffrey S Chamberlain, David P Corey, Martin J Aryee, J Keith Joung, Xandra O Breakefield, Casey A Maguire, Bence György
High levels of AAV vector integration into CRISPR-induced DNA breaks. Nature communications 10 (1) (2019)
Caleb A Lareau, Martin J Aryee
hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data. Nature methods 15 (3) (2019)
Huidong Chen, Luca Albergante, Jonathan Y Hsu, Caleb A Lareau, Giosue' Lo Bosco, Jihong Guan, Shuigeng Zhou, Alexander N Gorban, Daniel E Bauer, Martin J Aryee, David M Langenau, Andrei Zinovyev, Jason D Buenrostro, Guo-Cheng Yuan, Luca Pinello
Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nature communications 10 (1) (2019)
Benjamin P Kleinstiver, Alexander A Sousa, Russell T Walton, Y Esther Tak, Jonathan Y Hsu, Kendell Clement, Moira M Welch, Joy E Horng, Jose Malagon-Lopez, Irene Scarfo, Marcela V Maus, Luca Pinello, Martin J Aryee, J Keith Joung
Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nature biotechnology 37 (3) (2019)
Divy Kangeyan, Andrew Dunford, Sowmya Iyer, Chip Stewart, Megan Hanna, Gad Getz, Martin J Aryee
A (fire)cloud-based DNA methylation data preprocessing and quality control platform. BMC bioinformatics 20 (1) (2019)
Caleb A Lareau, M Kendell Clement, Jonathan Y Hsu, Vikram Pattanayak, J Keith Joung, Martin J Aryee, Luca Pinello
Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo". Nature methods 15 (4) (2018)
Richard C Pelikan, Jennifer A Kelly, Yao Fu, Caleb A Lareau, Kandice L Tessneer, Graham B Wiley, Mandi M Wiley, Stuart B Glenn, John B Harley, Joel M Guthridge, Judith A James, Martin J Aryee, Courtney Montgomery, Patrick M Gaffney
Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks. Nature communications 9 (1) (2018)
Akpéli V Nordor, Djamel Nehar-Belaid, Sophie Richon, David Klatzmann, Dominique Bellet, Virginie Dangles-Marie, Thierry Fournier, Martin J Aryee
The early pregnancy placenta foreshadows DNA methylation alterations of solid tumors. Epigenetics 12 (9) (2017)
Shengdar Q Tsai, Ved V Topkar, J Keith Joung, Martin J Aryee
Open-source guideseq software for analysis of GUIDE-seq data. Nature biotechnology 34 (5) (2017)
Shengdar Q Tsai, Nhu T Nguyen, Jose Malagon-Lopez, Ved V Topkar, Martin J Aryee, J Keith Joung
CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets. Nature methods 14 (6) (2017)
Benjamin P Kleinstiver, Shengdar Q Tsai, Michelle S Prew, Nhu T Nguyen, Moira M Welch, Jose M Lopez, Zachary R McCaw, Martin J Aryee, J Keith Joung
Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells. Nature biotechnology 34 (8) (2016)
Michael J Ziller, Kasper D Hansen, Alexander Meissner, Martin J Aryee
Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing. Nature methods 12 (3) (2014)
James Zou, Christoph Lippert, David Heckerman, Martin J Aryee, Jennifer Listgarten
Epigenome-wide association studies without the need for cell-type composition. Nature methods 11 (3) (2014)

Martin J Aryee.css-eqlu8i{font-size:small;padding-left:4px;} (Martin Aryee)

Publication Activity (10 Years)

Top Topics

Top Venues

Martin J Aryee (Martin Aryee)