Rahul Satija

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 40

Top Topics

Top Venues

bioRxiv : the preprint server for biology

Nature biotechnology

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

Publications

Austin Hartman, Rahul Satija
Comparative analysis of multiplexed in situ gene expression profiling technologies. bioRxiv : the preprint server for biology (2024)
Austin Hartman, Rahul Satija
Comparative analysis of multiplexed in situ gene expression profiling technologies. bioRxiv : the preprint server for biology (2024)
John D Blair, Austin Hartman, Fides Zenk, Carol Dalgarno, Barbara Treutlein, Rahul Satija
Phospho-seq: Integrated, multi-modal profiling of intracellular protein dynamics in single cells. bioRxiv : the preprint server for biology (2023)
Alev Baysoy, Zhiliang Bai, Rahul Satija, Rong Fan
The technological landscape and applications of single-cell multi-omics. Nature reviews. Molecular cell biology (2023)
Madeline H Kowalski, Hans-Hermann Wessels, Johannes Linder, Saket Choudhary, Austin Hartman, Yuhan Hao, Isabella Mascio, Carol Dalgarno, Anshul Kundaje, Rahul Satija
CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators. bioRxiv : the preprint server for biology (2023)
Bingjie Zhang, Rabi Upadhyay, Yuhan Hao, Marie I Samanovic, Ramin Sedaghat Herati, John D Blair, Jordan E Axelrad, Mark J Mulligan, Dan R Littman, Rahul Satija
Multimodal single-cell datasets characterize antigen-specific CD8 + T cells across SARS-CoV-2 vaccination and infection. Nature immunology (2023)
Bingjie Zhang, Rabi Upadhyay, Yuhan Hao, Marie I Samanovic, Ramin Sedaghat Herati, John D Blair, Jordan E Axelrad, Mark J Mulligan, Dan R Littman, Rahul Satija
Multimodal characterization of antigen-specific CD8 + T cells across SARS-CoV-2 vaccination and infection. bioRxiv : the preprint server for biology (2023)
Blue B Lake, Rajasree Menon, Seth Winfree, Qiwen Hu, Ricardo Melo Ferreira, Kian Kalhor, Daria Barwinska, Edgar A Otto, Michael Ferkowicz, Dinh Diep, Nongluk Plongthongkum, Amanda Knoten, Sarah Urata, Laura H Mariani, Abhijit S Naik, Sean Eddy, Bo Zhang, Yan Wu, Diane Salamon, James C Williams, Xin Wang, Karol S Balderrama, Paul J Hoover, Evan Murray, Jamie L Marshall, Teia Noel, Anitha Vijayan, Austin Hartman, Fei Chen, Sushrut S Waikar, Sylvia E Rosas, Francis Perry Wilson, Susan T Crowley, Krzysztof Kiryluk, John R Sedor, Robert D Toto, Chirag R Parikh, Eric H Kim, Rahul Satija, Anna Greka, Evan Z Macosko, Peter V Kharchenko, Joseph P Gaut, Jeffrey B Hodgin, null null, Michael T Eadon, Pierre C Dagher, Tarek M El-Achkar, Kun Zhang, Matthias Kretzler, Sanjay Jain
An atlas of healthy and injured cell states and niches in the human kidney. Nature 619 (7970) (2023)
Yuhan Hao, Tim Stuart, Madeline H Kowalski, Saket Choudhary, Paul J Hoffman, Austin Hartman, Avi Srivastava, Gesmira Molla, Shaista Madad, Carlos Fernandez-Granda, Rahul Satija
Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nature biotechnology (2023)
Bingjie Zhang, Rabi Upadhyay, Yuhan Hao, Marie I Samanovic, Ramin Sedaghat Herati, John D Blair, Jordan E Axelrad, Mark J Mulligan, Dan R Littman, Rahul Satija
Multimodal characterization of antigen-specific CD8 + T cells across SARS-CoV-2 vaccination and infection. bioRxiv : the preprint server for biology (2023)
Madeline H Kowalski, Hans-Hermann Wessels, Johannes Linder, Saket Choudhary, Austin Hartman, Yuhan Hao, Isabella Mascio, Carol Dalgarno, Anshul Kundaje, Rahul Satija
CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators. bioRxiv : the preprint server for biology (2023)
Bingjie Zhang, Rabi Upadhyay, Yuhan Hao, Marie I Samanovic, Ramin Sedaghat Herati, John D Blair, Jordan E Axelrad, Mark J Mulligan, Dan R Littman, Rahul Satija
Multimodal characterization of antigen-specific CD8 + T cells across SARS-CoV-2 vaccination and infection. bioRxiv : the preprint server for biology (2023)
Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Yuhan Hao, Efthymia Papalexi, William M Mauck, Lu Lu, John A Morris, Eleni P Mimitou, Peter Smibert, Neville E Sanjana, Rahul Satija
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq. Nature methods 20 (1) (2022)
Saket Choudhary, Rahul Satija
Comparison and evaluation of statistical error models for scRNA-seq. Genome biology 23 (1) (2022)
Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Yuhan Hao, Efthymia Papalexi, William M Mauck, Lu Lu, John A Morris, Eleni P Mimitou, Peter Smibert, Neville E Sanjana, Rahul Satija
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq. Nature methods (2022)
Bingjie Zhang, Avi Srivastava, Eleni P Mimitou, Tim Stuart, Ivan Raimondi, Yuhan Hao, Peter Smibert, Rahul Satija
Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro. Nature biotechnology 40 (8) (2022)
Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Yuhan Hao, Efthymia Papalexi, William M Mauck, Lu Lu, John A Morris, Eleni P Mimitou, Peter Smibert, Neville E Sanjana, Rahul Satija
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq. Nature methods 20 (1) (2022)
Tim Stuart, Stephanie Hao, Bingjie Zhang, Levan Mekerishvili, Dan A Landau, Silas Maniatis, Rahul Satija, Ivan Raimondi
Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution. Nature biotechnology (2022)
Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Yuhan Hao, Efthymia Papalexi, William M Mauck, Lu Lu, John A Morris, Eleni P Mimitou, Peter Smibert, Neville E Sanjana, Rahul Satija
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq. Nature methods 20 (1) (2022)
Tim Stuart, Stephanie Hao, Bingjie Zhang, Levan Mekerishvili, Dan A Landau, Silas Maniatis, Rahul Satija, Ivan Raimondi
Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution. Nature biotechnology (2022)
Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Yuhan Hao, Efthymia Papalexi, William M Mauck, Lu Lu, John A Morris, Eleni P Mimitou, Peter Smibert, Neville E Sanjana, Rahul Satija
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq. Nature methods 20 (1) (2022)
Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Yuhan Hao, Efthymia Papalexi, William M Mauck, Lu Lu, John A Morris, Eleni P Mimitou, Peter Smibert, Neville E Sanjana, Rahul Satija
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq. Nature methods 20 (1) (2022)
Kerstin B Kaufmann, Andy G X Zeng, Etienne Coyaud, Laura Garcia-Prat, Efthymia Papalexi, Alex Murison, Estelle M N Laurent, Michelle Chan-Seng-Yue, Olga I Gan, Kristele Pan, Jessica McLeod, Héléna Boutzen, Sasan Zandi, Shin-Ichiro Takayanagi, Rahul Satija, Brian Raught, Stephanie Z Xie, John E Dick
A latent subset of human hematopoietic stem cells resists regenerative stress to preserve stemness. Nature immunology 22 (6) (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)
Tim Stuart, Avi Srivastava, Shaista Madad, Caleb A Lareau, Rahul Satija
Single-cell chromatin state analysis with Signac. Nature methods 18 (11) (2021)
Efthymia Papalexi, Eleni P Mimitou, Andrew W Butler, Samantha Foster, Bernadette Bracken, William M Mauck, Hans-Hermann Wessels, Yuhan Hao, Bertrand Z Yeung, Peter Smibert, Rahul Satija
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens. Nature genetics 53 (3) (2021)
Muzlifah A Haniffa, Deanne M Taylor, Sten Linnarsson, Bruce J Aronow, Gary D Baider, Roger A Barker, Pablo G Camara, J Gray Camp, Alain Chédotal, Andrew J Copp, Heather C Etchevers, Paolo Giacobini, Berthold Göttgens, Guoji Guo, Ania Hupalowska, Kylie R James, Emily Kirby, Arnold R Kriegstein, Joakim Lundeberg, John C Marioni, Kerstin B Meyer, Kathy K Niakan, Mats Nilsson, Bayanne Olabi, Dana Pe'er, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Rahul Satija, Sarah A Teichmann, Barbara Treutlein, Roser Vento-Tormo, Simone Webb, null null
A roadmap for the Human Developmental Cell Atlas. Nature 597 (7875) (2021)
Igor Mandric, Tommer Schwarz, Arunabha Majumdar, Kangcheng Hou, Leah Briscoe, Richard Perez, Meena Subramaniam, Christoph Hafemeister, Rahul Satija, Chun Jimmie Ye, Bogdan Pasaniuc, Eran Halperin
Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis. Nature communications 11 (1) (2020)
Eleni P Mimitou, Anthony Cheng, Antonino Montalbano, Stephanie Hao, Marlon Stoeckius, Mateusz Legut, Timothy Roush, Alberto Herrera, Efthymia Papalexi, Zhengqing Ouyang, Rahul Satija, Neville E Sanjana, Sergei B Koralov, Peter Smibert
Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells. Nature methods 16 (5) (2019)
Tim Stuart, Rahul Satija
Integrative single-cell analysis. Nature reviews. Genetics 20 (5) (2019)
Wei Wang, Xiang Niu, Tim Stuart, Estelle Jullian, William M Mauck, Robert G Kelly, Rahul Satija, Lionel A Christiaen
A single-cell transcriptional roadmap for cardiopharyngeal fate diversification. Nature cell biology 21 (6) (2019)
Christoph Hafemeister, Rahul Satija
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome biology 20 (1) (2019)
William Stephenson, Laura T Donlin, Andrew W Butler, Cristina Rozo, Bernadette Bracken, Ali Rashidfarrokhi, Susan M Goodman, Lionel B Ivashkiv, Vivian P Bykerk, Dana E Orange, Robert B Darnell, Harold P Swerdlow, Rahul Satija
Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation. Nature communications 9 (1) (2018)
Marlon Stoeckius, Shiwei Zheng, Brian Houck-Loomis, Stephanie Hao, Bertrand Z Yeung, William M Mauck, Peter Smibert, Rahul Satija
Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. Genome biology 19 (1) (2018)
Samik Upadhaya, Katherine M Sawai, Efthymia Papalexi, Ali Rashidfarrokhi, Geunhyo Jang, Pratip Chattopadhyay, Rahul Satija, Boris Reizis
Kinetics of adult hematopoietic stem cell differentiation in vivo. The Journal of experimental medicine 215 (11) (2018)
Shiwei Zheng, Efthymia Papalexi, Andrew Butler, William Stephenson, Rahul Satija
Molecular transitions in early progenitors during human cord blood hematopoiesis. Molecular systems biology 14 (3) (2018)
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija
Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nature biotechnology 36 (5) (2018)
Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian R Loomis, Pratip K Chattopadhyay, Harold P Swerdlow, Rahul Satija, Peter Smibert
Simultaneous epitope and transcriptome measurement in single cells. Nature methods 14 (9) (2017)
Alexandra-Chloé Villani, Rahul Satija, Gary Reynolds, Siranush Sarkizova, Karthik Shekhar, James Fletcher, Morgane Griesbeck, Andrew W Butler, Shiwei Zheng, Suzan Lazo, Laura Jardine, David Dixon, Emily Stephenson, Emil Nilsson, Ida Grundberg, David McDonald, Andrew Filby, Weibo Li, Philip L De Jager, Orit Rozenblatt-Rosen, Andrew A Lane, Muzlifah A Haniffa, Aviv Regev, Nir Hacohen
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science (New York, N.Y.) 356 (6335) (2017)
Aviv Regev, Sarah A Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carnici, Menna Clatworthy, Hans Clevers, Bart Deplancke, Ian Dunham, James Eberwine, Roland Eils, Wolfgang Enard, Andrew Farmer, Lars Fugger, Berthold Göttgens, Nir Hacohen, Muzlifah A Haniffa, Martin Hemberg, Seung Kim, Paul Klenerman, Arnold Kriegstein, Ed S Lein, Sten Linnarsson, Emma Lundberg, Joakim Lundeberg, Partha Majumder, John C Marioni, Miriam Merad, Musa Mhlanga, Martijn Nawijn, Mihai Netea, Garry Nolan, Dana Pe'er, Anthony Phillipakis, Chris Paul Ponting, Stephen Quake, Wolf Reik, Orit Rozenblatt-Rosen, Joshua R Sanes, Rahul Satija, Ton N Schumacher, Alex Shalek, Ehud Shapiro, Padmanee Sharma, Jay W Shin, Oliver Stegle, Michael Stratton, Michael J T Stubbington, Fabian J Theis, Matthias Uhlen, Alexander van Oudenaarden, Allon Wagner, Fiona M Watt, Jonathan S Weissman, Barbara Wold, Ramnik Xavier, Nir Yosef, null null
The Human Cell Atlas. eLife 6 (2017)