T
Tyler Burks
Researcher at Broad Institute
Publications - 8
Citations - 2969
Tyler Burks is an academic researcher from Broad Institute. The author has contributed to research in topics: RNA & Gene. The author has an hindex of 6, co-authored 8 publications receiving 2114 citations.
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Journal ArticleDOI
Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens
Atray Dixit,Atray Dixit,Oren Parnas,Biyu Li,Jenny Chen,Jenny Chen,Charles P. Fulco,Charles P. Fulco,Livnat Jerby-Arnon,Nemanja D. Marjanovic,Nemanja D. Marjanovic,Danielle Dionne,Tyler Burks,Raktima Raychowdhury,Britt Adamson,Thomas M. Norman,Eric S. Lander,Eric S. Lander,Eric S. Lander,Jonathan S. Weissman,Jonathan S. Weissman,Nir Friedman,Nir Friedman,Aviv Regev,Aviv Regev,Aviv Regev +25 more
TL;DR: Perturb-seq as discussed by the authors combines single-cell RNA sequencing and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool.
Journal ArticleDOI
Massively-parallel single nucleus RNA-seq with DroNc-seq
Naomi Habib,Naomi Habib,Inbal Avraham-Davidi,Anindita Basu,Tyler Burks,Karthik Shekhar,Matan Hofree,Sourav Choudhury,Sourav Choudhury,François Aguet,Ellen Gelfand,Kristin Ardlie,David A. Weitz,Orit Rozenblatt-Rosen,Feng Zhang,Feng Zhang,Aviv Regev,Aviv Regev +17 more
TL;DR: In this paper, a massively parallel single-nucleus RNA sequencing (sNuc-seq) with droplet technology is proposed. But it does not provide high throughput, and it is not suitable for high-dimensional data.
Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens
Atray Dixit,Atray Dixit,Oren Parnas,Biyu Li,Jenny Chen,Jenny Chen,Charles P. Fulco,Charles P. Fulco,Livnat Jerby-Arnon,Nemanja D. Marjanovic,Nemanja D. Marjanovic,Danielle Dionne,Tyler Burks,Raktima Raychowdhury,Britt Adamson,Thomas M. Norman,Eric S. Lander,Eric S. Lander,Eric S. Lander,Jonathan S. Weissman,Jonathan S. Weissman,Nir Friedman,Nir Friedman,Aviv Regev,Aviv Regev,Aviv Regev +25 more
TL;DR: Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions, and posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation.
Journal ArticleDOI
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods.
Jiarui Ding,Xian Adiconis,Sean Simmons,Monika S. Kowalczyk,Cynthia C. Hession,Nemanja D. Marjanovic,Travis K. Hughes,Marc H. Wadsworth,Tyler Burks,Lan T. Nguyen,John Y. Kwon,Boaz Barak,William Ge,Amanda J. Kedaigle,Shaina Carroll,Shuqiang Li,Nir Hacohen,Nir Hacohen,Orit Rozenblatt-Rosen,Alex K. Shalek,Alexandra-Chloé Villani,Alexandra-Chloé Villani,Aviv Regev,Aviv Regev,Joshua Z. Levin +24 more
TL;DR: To directly compare the methods and avoid processing differences introduced by the existing pipelines, scumi is developed, a flexible computational pipeline that can be used with any single-cell RNA-sequencing method.
Posted ContentDOI
Systematic comparative analysis of single cell RNA-sequencing methods
Jiarui Ding,Xian Adiconis,Sean Simmons,Monika S. Kowalczyk,Cynthia C. Hession,Nemanja D. Marjanovic,Travis K. Hughes,Marc H. Wadsworth,Tyler Burks,Lan T. Nguyen,John Y. Kwon,Boaz Barak,William Ge,Amanda J. Kedaigle,Shaina Carroll,Shuqiang Li,Nir Hacohen,Nir Hacohen,Orit Rozenblatt-Rosen,Alex K. Shalek,Alexandra-Chloé Villani,Alexandra-Chloé Villani,Aviv Regev,Aviv Regev,Joshua Z. Levin +24 more
TL;DR: This study directly compares seven methods for single cell and/or single nucleus profiling from three types of samples, generating 36 libraries in six separate experiments in a single center and developed and applied scumi, a flexible computational pipeline that can be used for any scRNA-seq method.