Publications

17 Results (Filters Applied)

Innovation Lab x

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 Biotechnology 2021 Apr. 29.

Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens.

Noa Liscovitch-Brauer, Antonino Montalbano, Jiale Deng, Alejandro Méndez-Mancilla, Hans-Hermann Wessels, Nicholas G. Moss, Chia-Yu Kung, Akash Sookdeo, Xinyi Guo, Evan Geller, Suma Jaini, Peter Smibert & Neville E. Sanjana

eLife 2021 Apr. 16.

Improving oligo-conjugated antibody signal in multimodal single-cell analysis.

Terkild Brink Buus, Alberto Herrera, , Eleni Mimitou, Anthony Cheng, Ramin Herati, , Peter Smibert, Niels Odum, Sergei B Koralov

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

Nature Structural & Molecular Biology. 2021 Jan. 4.

Structural and functional characterization of the Spo11 core complex.

Corentin Claeys Bouuaert, Sam E. Tischfield, Stephen Pu, Eleni P. Mimitou, Ernesto Arias-Palomo, James M. Berger & Scott Keeney

Nature Communications. 2020 Apr. 20.

High throughput pMHC-I tetramer library production using chaperone-mediated peptide exchange.

Sarah A. Overall, Jugmohit S. Toor, Stephanie Hao, Mark Yarmarkovich, Sara M. O’Rourke, Giora I. Morozov, Son Nguyen, Alberto Sada Japp, Nicolas Gonzalez, Danai Moschidi, Michael R. Betts, John M. Maris, Peter Smibert & Nikolaos G. Sgourakis

2019 Aug. 26.

Low SATB1 expression promotes IL-5 and IL-9 expression in Sezary Syndrome.

Herrera A, Fredholm S, Cheng A, Mimitou EP, Seffens A, Bar-Natan M, Sun A, Latkowski J, Willerslew-Olsen A, Buus TB, Gluud M, Krejsgaard T, Torres-Rusillo S, Bonefeld CM, Woetmann A, Geisler C, Geskin LJ, Ouyang Z, Smibert P, Ødum N, Koralov SB.

Cell. 2019 June 6.

Comprehensive Integration of Single-Cell Data.

Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WH, Hao Y, Stoeckius M, Smibert P, Satija R.

Nature Methods. 2019 Apr 22.

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells.

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.

Nucleic Acids Res. 2018 Nov 30

Single-cell stabilization method identifies gonadotrope transcriptional dynamics and pituitary cell type heterogeneity.

Ruf-Zamojski F, Ge Y, Nair V, Zamojski M, Pincas H, Toufaily C, Tome-Garcia J, Stoeckius M, Stephenson W, Smith GR, Bernard DJ, Tsankova NM, Hartmann BM, Fribourg M, Smibert P, Swerdlow H, Turgeon JL, Sealfon SC.

Nature. 2019 July 3.

Somatic mutations and cell identity linked by Genotyping of Transcriptomes

Nam AS, Kim K-T, Chaligne R, Izzo F, Ang C, Abu-Zeinah G, Omans ND, Pastore A, Taylor J, Alonso A, Mariani M, Cubillos-Ruiz JR, Tam W, Hoffman R, .Scandura, JM, Rabadan R, Abdel-Wahab O, Smibert P, Landau DA.

Micro and Nano Systems Letters. 2018 June 21.

High-throughput magnetic particle washing in nanoliter droplets using serial injection and splitting.

Stephenson W.

Proc Natl Acad Sci U S A. 2018 June 6.

YES1 amplification is a mechanism of acquired resistance to EGFR inhibitors identified by transposon mutagenesis and clinical genomics.

Fan PD, Narzisi G, Jayaprakash AD, Venturini E, Robine N, Smibert P, Germer S, Yu HA, Jordan EJ, Paik PK, Janjigian YY, Chaft JE, Wang L, Jungbluth AA, Middha S, Spraggon L, Qiao H, Lovly CM, Kris MG, Riely GJ, Politi K, Varmus H, Ladanyi M.

Nature Communications. 2018 Feb. 23.

Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation.

Stephenson W, Donlin LT, Butler A, Rozo C, Bracken B, Rashidfarrokhi A, Goodman SM, Ivashkiv LB, Bykerk VP, Orange DE, Darnell RB, Swerdlow HP, Satija R.

Nature Methods. 2017 July 31.

Large-scale simultaneous measurement of epitopes and transcriptomes in single cells

Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Swerdlow H, Satija R, Smibert, P

Genome Biology. 2018 Dec. 19.

Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics.

Stoeckius M, Zheng S, Houck-Loomis, B, Hao S, Yeung B, Smibert P, Satija R.

PRE-PRINT PUBLICATIONS

bioRxiv. 2021 Apr. 8

Discovery of target genes and pathways of blood trait loci using pooled CRISPR screens and single cell RNA sequencing.

John A Morris, Zharko Daniloski, Júlia Domingo, Timothy Barry, Marcello Ziosi, Dafni A Glinos, Stephanie Hao, Eleni Mimitou, Peter Smibert, Kathryn Roeder, Eugene Katsevich, Tuuli Lappalainen, Neville E Sanjana

bioRxiv. 2020 Dec. 24.

Single cell analysis of blood mononuclear cells stimulated through CD3 and CD28 shows collateral activation of B and NK cells and demise of monocytes.

Nathan Lawlor, Djamel Nehar-Belaid, Jessica D.S. Grassmann, Marlon Stoeckius, Peter Smibert, Michael L. Stitzel, Virginia Pascual, Jacques Banchereau, Adam Williams, Duygu Ucar

bioRxiv. 2020 Sept. 29.

The functional and phenotypic diversity of single T-cell infiltrates in human colorectal cancer as correlated with clinical outcome.

Kazuya Masuda, Adam Kornberg, , , Kerim Secener, , Alyssa M Bacarella, Matthew Ingham, Vilma Rosario, Ahmed M Al-Masrou, , P.Ravi Kiran, Kelley S Yan, Marlon Stoeckius, Peter Smibert, Paul E Oberstein, Peter A Sims,

bioRxiv. 2020 Sept. 8.

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

Eleni P Mimitou, Caleb A Lareau, Kelvin Y Chen, Andre L Zorzetto-Fernandes, Yusuke Takeshima, Wendy Luo, Tse-Shun Huang, Bertrand Yeung, Pratiksha I Thakore, James Badger Wing, Kristopher L Nazor, Shimon Sakaguchi, Leif S Ludwig, Vijay G Sankaran, Aviv Regev, Peter Smibert

bioRxiv. 2020 June 16.

Improving oligo-conjugated antibody signal in multimodal single-cell analysis.

Terkild Brink Buus, Alberto Herrera, Ellie Ivanova, Eleni Mimitou, Anthony Cheng, Thales Papagiannakopoulos, Peter Smibert, Niels Ødum, Sergei B. Koralov

bioRxiv. 2020 June 1.

Direct detection of RNA modifications and structure using single molecule nanopore sequencing.

William Stephenson, Roham Razaghi, Steven Busan, Kevin M. Weeks, Winston Timp, Peter Smibert.

Faculty labs

NYGC Labs

Publications

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

Integrated analysis of multimodal single-cell data.

Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens.

Improving oligo-conjugated antibody signal in multimodal single-cell analysis.

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

Structural and functional characterization of the Spo11 core complex.

High throughput pMHC-I tetramer library production using chaperone-mediated peptide exchange.

Low SATB1 expression promotes IL-5 and IL-9 expression in Sezary Syndrome.

Comprehensive Integration of Single-Cell Data.

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells.

Single-cell stabilization method identifies gonadotrope transcriptional dynamics and pituitary cell type heterogeneity.

Somatic mutations and cell identity linked by Genotyping of Transcriptomes

High-throughput magnetic particle washing in nanoliter droplets using serial injection and splitting.

YES1 amplification is a mechanism of acquired resistance to EGFR inhibitors identified by transposon mutagenesis and clinical genomics.

Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation.

Large-scale simultaneous measurement of epitopes and transcriptomes in single cells

Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics.