Publications

40 Results (Filters Applied)

Satija Lab x

Nature Biotechnology. 2023 May 25.

Dictionary learning for integrative, multimodal and scalable single-cell analysis.

Yuhan Hao, Tim Stuart, Madeline H. Kowalski, Saket Choudhary, Paul Hoffman, Austin Hartman, Avi Srivastava, Gesmira Molla, Shaista Madad, Carlos Fernandez-Granda & Rahul Satija

Nature Methods 2022 Dec. 22.

Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq.

Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Yuhan Hao, Efthymia Papalexi, William M. Mauck III, Lu Lu, John A. Morris, Eleni P. Mimitou, Peter Smibert, Neville E. Sanjana & Rahul Satija

Nature Biotechnology. 2022 Dec. 19.

Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution.

Tim Stuart, Stephanie Hao, Bingjie Zhang, Levan Mekerishvili, Dan A. Landau, Silas Maniatis, Rahul Satija & Ivan Raimondi

Nature Biotechnology. 2022 March 24.

Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro

Bingjie Zhang, Avi Srivastava, Eleni Mimitou, Tim Stuart, Ivan Raimondi, Yuhan Hao, Peter Smibert & Rahul Satija

Cell Genomics. 2022 March 9.

Single nucleus multi-omics identifies human cortical cell regulatory genome diversity.

Chongyuan Luo, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, Wayne I. Doyle, Tim Stuart, Rebecca D. Hodge, Lijuan Hu, Bang-An Wang, Zhuzhu Zhang, Sebastian Preissl, Dong-Sung Lee, Jingtian Zhou, Sheng-Yong Niu, Rosa Castanon, Anna Bartlett, Angeline Rivkin, Xinxin Wang, Jacinta Lucero, Joseph R. Nery, David A. Davis, Deborah C. Mash, Rahul Satija, Jesse R. Dixon, Sten Linnarsson, Ed Lein, M. Margarita Behrens, Bing Ren, Eran A. Mukamel, Joseph R. Ecker

Genome Biology. 2022 Jan. 18.

Comparison and evaluation of statistical error models for scRNA-seq.

Choudhary S, Satija R.

Genome Biology. 2021 Dec. 6.

geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq.

Missarova A, Jain J, Butler A, Ghazanfar S, Stuart T, Brusko M, Wasserfall C, Nick H, Brusko T, Atkinson M, Satija R, Marioni JC.

The Plant Cell. 2021 Nov. 15

Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems.

Simon C Groen, Zoe Joly-Lopez, Adrian E Platts, Mignon Natividad, Zoe Fresquez, William M Mauck III, Marinell R Quintana, Carlo LU Cabral, Rolando O Torres, Rahul Satija, Michael D Purugganan, Amelia Henry

Nature Methods. 2021`Nov. 1.

Single-cell chromatin state analysis with Signac.

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

Nature. 2021 Sept. 8.

A roadmap for the Human Developmental Cell Atlas.

Haniffa M, Taylor D, Linnarsson S, Aronow BJ, Bader GD, Barker RA, Camara PG, Camp JG, Chédotal A, Copp A, Etchevers HC, Giacobini P, Göttgens B, Guo G, Hupalowska A, James KR, Kirby E, Kriegstein A, Lundeberg J, Marioni JC, Meyer KB, Niakan KK, Nilsson M, Olabi B, Pe’er D, Regev A, Rood J, Rozenblatt-Rosen O, Satija R, Teichmann SA, Treutlein B, Vento-Tormo R, Webb S; Human Cell Atlas Developmental Biological Network.

Nature Biotechnology. 2021 June 3.

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.

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

Cell. 2021 May 31.

Integrated analysis of multimodal single-cell data.

Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M. Mauck, Shiwei Zheng, Andrew Butler, Maddie Jane Lee, Aaron J. Wilk, Charlotte Darby, Michael Zagar, Paul Hoffman, Marlon Stoeckius, Efthymia Papalexi, Eleni P. Mimitou, Jaison Jain, Avi Srivastava, Tim Stuart, Lamar B. Fleming, Bertrand Yeung, Angela J. Rogers, Juliana M. McElrath, Catherine A. Blish, Raphael Gottardo, Peter Smibert, Rahul Satija

Nature Immunology. 2021 May 6.

A latent subset of human hematopoietic stem cells resists regenerative stress to preserve stemness.

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

Nature Genetics. 2021 Mar. 1.

Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens.

Efthymia Papalexi, Eleni P. Mimitou, Andrew W. Butler, Samantha Foster, Bernadette Bracken, William M. Mauck III, Hans-Hermann Wessels, Yuhan Hao, Bertrand Z. Yeung, Peter Smibert & Rahul Satija

Bioinformatics. 2021 Jan. 20.

Compression of quantification uncertainty for scRNA-seq counts.

Van Buren S, Sarkar H, Srivastava A, Rashid NU, Patro R, Love MI.

PLOS Computational Biology. 2021 Jan 11.

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data.

Soneson C, Srivastava A, Patro R, Stadler MB.

Nature Communications. 2020 Oct. 30.

Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis.

Mandric I, Schwarz T, Majumdar A, Hou K, Briscoe L, Perez R, Subramaniam M, Hafemeister C, Satija R, Ye CJ, Pasaniuc B, Halperin E.

Cell. 2020 June 24.

Niche-Selective Inhibition of Pathogenic Th17 Cells by Targeting Metabolic Redundancy.

Wu L, Hollinshead KER, Hao Y, Au C, Kroehling L, Ng C, Lin WY, Li D, Silva HM, Shin J, Lafaille JJ, Possemato R, Pacold ME, Papagiannakopoulos T, Kimmelman AC, Satija R, Littman DR.

PRE-PRINT PUBLICATIONS

bioRxiv. 2023 March 27.

Accounting for fragments of unexpected origin improves transcript quantification in RNA-seq simulations focused on increased realism.

Avi Srivastava, Mohsen Zakeri, Hirak Sarkar, Charlotte Soneson, Carl Kingsford, Rob Patro

Faculty Labs

NYGC Labs