Luca Pinello

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 39

Top Venues

Nature genetics

bioRxiv : the preprint server for biology

Research square

Nature methods

Broad Institute

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

Affiliation History

Broad Institute Nov 08 2017

United States

Associate Member

Massachusetts General Hospital / Harvard Medical School Oct 01 2016

United States

Assistant Professor :: Molecular Pathology & Cancer Center

Publications

Jayoung Ryu, Sam Barkal, Tian Yu, Martin Jankowiak, Yunzhuo Zhou, Matthew Francoeur, Quang Vinh Phan, Zhijian Li, Manuel Tognon, Lara Brown, Michael I Love, Vineel Bhat, Guillaume Lettre, David Benjamin Ascher, Christopher A Cassa, Richard I Sherwood, Luca Pinello
Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. Nature genetics (2024)
Malte Daniel Luecken, Scott A Gigante, Daniel B Burkhardt, Robrecht Cannoodt, Daniel C Strobl, Nikolay S Markov, Luke Zappia, Giovanni Palla, Wesley Lewis, Daniel Dimitrov, Michael E Vinyard, D S Magruder, Alma Andersson, Emma Dann, Qian Qin, Dominik J Otto, Michal Klein, Olga Borisovna Botvinnik, Louise Deconinck, Kai Waldrant, null null, Jonathan M Bloom, Angela Oliveira Pisco, Julio Saez-Rodriguez, Drausin Wulsin, Luca Pinello, Yvan Saeys, Fabian Joachim Theis, Smita Krishnaswamy
Defining and benchmarking open problems in single-cell analysis. Research square (2024)
Y Esther Tak, Jonathan Y Hsu, Justine Shih, Hayley T Schultz, Ivy T Nguyen, Kin Chung Lam, Luca Pinello, J Keith Joung
CRISPR PERSIST-On enables heritable and fine-tunable human gene activation. bioRxiv : the preprint server for biology (2024)
Jayoung Ryu, Sam Barkal, Tian Yu, Martin Jankowiak, Yunzhuo Zhou, Matthew Francoeur, Quang Vinh Phan, Zhijian Li, Manuel Tognon, Lara Brown, Michael I Love, Vineel Bhat, Guillaume Lettre, David Benjamin Ascher, Christopher A Cassa, Richard I Sherwood, Luca Pinello
Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. Nature genetics (2024)
Jayoung Ryu, Sam Barkal, Tian Yu, Martin Jankowiak, Yunzhuo Zhou, Matthew Francoeur, Quang Vinh Phan, Zhijian Li, Manuel Tognon, Lara Brown, Michael I Love, Vineel Bhat, Guillaume Lettre, David Benjamin Ascher, Christopher A Cassa, Richard I Sherwood, Luca Pinello
Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. Nature genetics (2024)
Malte Daniel Luecken, Scott A Gigante, Daniel B Burkhardt, Robrecht Cannoodt, Daniel C Strobl, Nikolay S Markov, Luke Zappia, Giovanni Palla, Wesley Lewis, Daniel Dimitrov, Michael E Vinyard, D S Magruder, Alma Andersson, Emma Dann, Qian Qin, Dominik J Otto, Michal Klein, Olga Borisovna Botvinnik, Louise Deconinck, Kai Waldrant, null null, Jonathan M Bloom, Angela Oliveira Pisco, Julio Saez-Rodriguez, Drausin Wulsin, Luca Pinello, Yvan Saeys, Fabian Joachim Theis, Smita Krishnaswamy
Defining and benchmarking open problems in single-cell analysis. Research square (2024)
Jayoung Ryu, Sam Barkal, Tian Yu, Martin Jankowiak, Yunzhuo Zhou, Matthew Francoeur, Quang Vinh Phan, Zhijian Li, Manuel Tognon, Lara Brown, Michael I Love, Vineel Bhat, Guillaume Lettre, David Benjamin Ascher, Christopher A Cassa, Richard I Sherwood, Luca Pinello
Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. Nature genetics 56 (5) (2024)
Alex R Lederer, Maxine Leonardi, Lorenzo Talamanca, Antonio Herrera, Colas Droin, Irina Khven, Hugo J F Carvalho, Alessandro Valente, Albert Dominguez Mantes, Pau Mulet Arabí, Luca Pinello, Felix Naef, Gioele La Manno
Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations. bioRxiv : the preprint server for biology (2024)
Jayoung Ryu, Sam Barkal, Tian Yu, Martin Jankowiak, Yunzhuo Zhou, Matthew Francoeur, Quang Vinh Phan, Zhijian Li, Manuel Tognon, Lara Brown, Michael I Love, Vineel Bhat, Guillaume Lettre, David Benjamin Ascher, Christopher A Cassa, Richard I Sherwood, Luca Pinello
Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. Nature genetics 56 (5) (2024)
Lucas Ferreira DaSilva, Simon Senan, Zain Munir Patel, Aniketh Janardhan Reddy, Sameer Gabbita, Zach Nussbaum, César Miguel Valdez Córdova, Aaron Wenteler, Noah Weber, Tin M Tunjic, Talha Ahmad Khan, Zelun Li, Cameron Smith, Matei Bejan, Lithin Karmel Louis, Paola Cornejo, Will Connell, Emily S Wong, Wouter Meuleman, Luca Pinello
DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements. bioRxiv : the preprint server for biology (2024)
Mahshid Rahmat, M Kendell Clement, Jean-Baptiste Alberge, Romanos Sklavenitis-Pistofidis, Rohan Kodgule, Charles P Fulco, Daniel Heilpern-Mallory, Katarina Nilsson, David M Dorfman, Jesse M Engreitz, Gad A Getz, Luca Pinello, Russell J H Ryan, Irene M Ghobrial
Selective Enhancer Gain of Function Deregulates MYC Expression in Multiple Myeloma. Cancer research (2024)
Jiecong Lin, Ruibang Luo, Luca Pinello
EPInformer: a scalable deep learning framework for gene expression prediction by integrating promoter-enhancer sequences with multimodal epigenomic data. bioRxiv : the preprint server for biology (2024)
Lucas Ferreira DaSilva, Simon Senan, Zain Munir Patel, Aniketh Janardhan Reddy, Sameer Gabbita, Zach Nussbaum, César Miguel Valdez Córdova, Aaron Wenteler, Noah Weber, Tin M Tunjic, Talha Ahmad Khan, Zelun Li, Cameron Smith, Matei Bejan, Lithin Karmel Louis, Paola Cornejo, Will Connell, Emily S Wong, Wouter Meuleman, Luca Pinello
DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements. bioRxiv : the preprint server for biology (2024)
Jayoung Ryu, Sam Barkal, Tian Yu, Martin Jankowiak, Yunzhuo Zhou, Matthew Francoeur, Quang Vinh Phan, Zhijian Li, Manuel Tognon, Lara Brown, Michael I Love, Vineel Bhat, Guillaume Lettre, David Benjamin Ascher, Christopher A Cassa, Richard I Sherwood, Luca Pinello
Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. Nature genetics 56 (5) (2024)
Lucas Ferreira DaSilva, Simon Senan, Zain Munir Patel, Aniketh Janardhan Reddy, Sameer Gabbita, Zach Nussbaum, César Miguel Valdez Córdova, Aaron Wenteler, Noah Weber, Tin M Tunjic, Talha Ahmad Khan, Zelun Li, Cameron Smith, Matei Bejan, Lithin Karmel Louis, Paola Cornejo, Will Connell, Emily S Wong, Wouter Meuleman, Luca Pinello
DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements. bioRxiv : the preprint server for biology (2024)
Jiecong Lin, Ruibang Luo, Luca Pinello
EPInformer: A Scalable Deep Learning Framework for Gene Expression Prediction by Integrating Promoter-enhancer Sequences with Multimodal Epigenomic Data. bioRxiv : the preprint server for biology (2024)
Jonathan Y Hsu, Kin Chung Lam, Justine Shih, Luca Pinello, J Keith Joung
MOSAIC enables in situ saturation mutagenesis of genes and CRISPR prime editing guide RNA optimization in human cells. bioRxiv : the preprint server for biology (2024)
Malte Daniel Luecken, Scott A Gigante, Daniel Burkhardt, Robrecht Cannoodt, Daniel Strobl, Nikolay Markov, Luke Zappia, Giovanni Palla, Wesley Lewis, Daniel Dimitrov, Michael Vinyard, Daniel Magruder, Alma Andersson, Emma Dann, Qian Qin, Dominik J Otto, Michal Klein, Olga Botvinnik, Louise Deconinck, Kai Waldrant, Bastian Rieck, Constantin Ahlmann-Eltze, Eduardo da Veiga Beltrame, Andrew Benz, Carmen Bravo González-Blas, Ann Chen, Benjamin DeMeo, Can Ergen, Swann Floc'hlay, Adam Gayoso, Stephanie C Hicks, Yuge Ji, Vitalii Kleshchevnikov, Gioele La Manno, Maximilian Lombardo, Romain Lopez, Dario Righelli, Hirak Sarkar, Valentine Svensson, Alexander Tong, Galen Xing, Chenling Xu, Jonathan Bloom, Angela Pisco, Julio Saez-Rodriguez, Drausin Wulsin, Luca Pinello, Yvan Saeys, Fabian Joachim Theis, Smita Krishnaswamy
Defining and benchmarking open problems in single-cell analysis. Research square (2024)
Lingfei Wang, Nikolaos Trasanidis, Ting Wu, Guanlan Dong, Michael Hu, Daniel E Bauer, Luca Pinello
Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics. Nature methods (2023)
Vedagopuram Sreekanth, Max Jan, Kevin Tianmeng Zhao, Donghyun Lim, Jessie R Davis, Marie McConkey, Veronica Kovalcik, Sam Barkal, Benjamin K Law, James D Fife, Ruilin Tian, Michael E Vinyard, Basheer Becerra, Martin Edward Kampmann, Richard I Sherwood, Luca Pinello, David R Liu, Benjamin L Ebert, Amit Choudhary
A molecular glue approach to control the half-life of CRISPR-based technologies. bioRxiv : the preprint server for biology (2023)
Huidong Chen, Jayoung Ryu, Michael E Vinyard, Adam Lerer, Luca Pinello
SIMBA: single-cell embedding along with features. Nature methods (2023)
Jayoung Ryu, Sam Barkal, Tian Yu, Martin Jankowiak, Yunzhuo Zhou, Matthew Francoeur, Quang Vinh Phan, Zhijian Li, Manuel Tognon, Lara Brown, Michael I Love, Guillaume Lettre, David B Ascher, Christopher A Cassa, Richard I Sherwood, Luca Pinello
Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. medRxiv : the preprint server for health sciences (2023)
Yun Wei, Qian Qin, Chuan Yan, Madeline N Hayes, Sara P Garcia, Haibin Xi, Daniel Do, Alexander H Jin, Tiffany C Eng, Karin M McCarthy, Abhinav Adhikari, Maristela L Onozato, Dimitrios Spentzos, Gunnlaugur P Neilsen, A John Iafrate, Leonard H Wexler, April D Pyle, Mario L Suvà, Filemon Dela Cruz, Luca Pinello, David M Langenau
Single-cell analysis and functional characterization uncover the stem cell hierarchies and developmental origins of rhabdomyosarcoma. Nature cancer 3 (8) (2022)
Kathleen A Christie, Jimmy A Guo, Rachel A Silverstein, Roman M Doll, Megumu Mabuchi, Hannah E Stutzman, Jiecong Lin, Linyuan Ma, Russell T Walton, Luca Pinello, Gregory Brett Robb, Benjamin P Kleinstiver
Precise DNA cleavage using CRISPR-SpRYgests. Nature biotechnology (2022)
Samuele Cancellieri, Jing Zeng, Linda Yingqi Lin, Manuel Tognon, My Anh Nguyen, Jiecong Lin, Nicola Bombieri, Stacy A Maitland, Marioara-Felicia Ciuculescu, Varun Katta, Shengdar Q Tsai, Myriam Armant, Scot A Wolfe, Rosalba Giugno, Daniel E Bauer, Luca Pinello
Human genetic diversity alters off-target outcomes of therapeutic gene editing. Nature genetics 55 (1) (2022)
Samuele Cancellieri, Jing Zeng, Linda Yingqi Lin, Manuel Tognon, My Anh Nguyen, Jiecong Lin, Nicola Bombieri, Stacy A Maitland, Marioara-Felicia Ciuculescu, Varun Katta, Shengdar Q Tsai, Myriam Armant, Scot A Wolfe, Rosalba Giugno, Daniel E Bauer, Luca Pinello
Human genetic diversity alters off-target outcomes of therapeutic gene editing. Nature genetics (2022)
Samuele Cancellieri, Jing Zeng, Linda Yingqi Lin, Manuel Tognon, My Anh Nguyen, Jiecong Lin, Nicola Bombieri, Stacy A Maitland, Marioara-Felicia Ciuculescu, Varun Katta, Shengdar Q Tsai, Myriam Armant, Scot A Wolfe, Rosalba Giugno, Daniel E Bauer, Luca Pinello
Human genetic diversity alters off-target outcomes of therapeutic gene editing. Nature genetics 55 (1) (2022)
Samuele Cancellieri, Jing Zeng, Linda Yingqi Lin, Manuel Tognon, My Anh Nguyen, Jiecong Lin, Nicola Bombieri, Stacy A Maitland, Marioara-Felicia Ciuculescu, Varun Katta, Shengdar Q Tsai, Myriam Armant, Scot A Wolfe, Rosalba Giugno, Daniel E Bauer, Luca Pinello
Human genetic diversity alters off-target outcomes of therapeutic gene editing. Nature genetics (2022)
Samuele Cancellieri, Jing Zeng, Linda Yingqi Lin, Manuel Tognon, My Anh Nguyen, Jiecong Lin, Nicola Bombieri, Stacy A Maitland, Marioara-Felicia Ciuculescu, Varun Katta, Shengdar Q Tsai, Myriam Armant, Scot A Wolfe, Rosalba Giugno, Daniel E Bauer, Luca Pinello
Human genetic diversity alters off-target outcomes of therapeutic gene editing. Nature genetics 55 (1) (2022)
Samuele Cancellieri, Jing Zeng, Linda Yingqi Lin, Manuel Tognon, My Anh Nguyen, Jiecong Lin, Nicola Bombieri, Stacy A Maitland, Marioara-Felicia Ciuculescu, Varun Katta, Shengdar Q Tsai, Myriam Armant, Scot A Wolfe, Rosalba Giugno, Daniel E Bauer, Luca Pinello
Human genetic diversity alters off-target outcomes of therapeutic gene editing. Nature genetics 55 (1) (2022)
Jonathan Y Hsu, Julian Grünewald, Regan N Szalay, Justine Shih, Andrew V Anzalone, Kin Chung Lam, Max W Shen, Karl Petri, David R Liu, J Keith Joung, Luca Pinello
PrimeDesign software for rapid and simplified design of prime editing guide RNAs. Nature communications 12 (1) (2021)
Nan Liu, Shuqian Xu, Qiuming Yao, Qian Zhu, Yan Kai, Jonathan Y Hsu, Phraew Sakon, Luca Pinello, Guo-Cheng Yuan, Daniel E Bauer, Stuart H Orkin
Transcription factor competition at the γ-globin promoters controls hemoglobin switching. Nature genetics 53 (4) (2021)
Jonathan Y Hsu, Charles P Fulco, Mitchel A Cole, Matthew C Canver, Danilo Pellin, Falak Sher, Rick Farouni, Kendell Clement, Jimmy A Guo, Luca Biasco, Stuart H Orkin, Jesse M Engreitz, Eric S Lander, J Keith Joung, Daniel E Bauer, Luca Pinello
CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data. Nature methods 15 (12) (2019)
Shuqian Xu, Kevin Luk, Qiuming Yao, Anne H Shen, Jing Zeng, Yuxuan Wu, Hong-Yuan Luo, Christian Brendel, Luca Pinello, David H K Chui, Scot A Wolfe, Daniel E Bauer
Editing aberrant splice sites efficiently restores β-globin expression in β-thalassemia. Blood 133 (21) (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)
Kendell Clement, Holly Rees, Matthew C Canver, Jason M Gehrke, Rick Farouni, Jonathan Y Hsu, Mitchel A Cole, David R Liu, J Keith Joung, Daniel E Bauer, Luca Pinello
CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nature biotechnology 37 (3) (2019)
Huidong Chen, Caleb Lareau, Tommaso Andreani, Michael E Vinyard, Sara P Garcia, Kendell Clement, Miguel A Andrade-Navarro, Jason D Buenrostro, Luca Pinello
Assessment of computational methods for the analysis of single-cell ATAC-seq data. Genome biology 20 (1) (2019)
Matthew C Canver, Maximilian Haeussler, Daniel E Bauer, Stuart H Orkin, Neville E Sanjana, Ophir Shalem, Guo-Cheng Yuan, Feng Zhang, Jean-Paul Concordet, Luca Pinello
Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments. Nature protocols 13 (5) (2018)
Qin Tang, Sowmya Iyer, Riadh Lobbardi, John C Moore, Huidong Chen, Caleb A Lareau, Christine Hebert, McKenzie L Shaw, Cyril Neftel, Mario L Suva, Yvonne J K Edwards, Andre Bernards, Martin Aryee, Luca Pinello, Iain A Drummond, David M Langenau
Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing. The Journal of experimental medicine 214 (10) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Luca Pinello