Selected Publications

Functional phenotyping of genomic variants using joint multiomic single-cell DNA-RNA sequencing.

Lindenhofer D, Bauman JR, Hawkins JA, Fitzgerald D, Yildiz U, Jung H, Korosteleva A, Marttinen M, Kueblbeck M, Zaugg JB, Noh KM, Dietrich S, Huber W, Stegle O, Steinmetz LM

Nature methods, 2025

doi:10.1038/s41592-025-02805-0.

Mislocalization of pathogenic RBM20 variants in dilated cardiomyopathy is caused by loss-of-interaction with Transportin-3.

Kornienko J, Rodríguez-Martínez M, Fenzl K, Hinze F, Schraivogel D, Grosch M, Tunaj B, Lindenhofer D, Schraft L, Kueblbeck M, Smith E, Mao C, Brown E, Owens A, Saguner AM, Meder B, Parikh V, Gotthardt M, Steinmetz LM

Nature communications, 2023

doi:10.1038/s41467-023-39965-6.

Striated muscle-specific base editing enables correction of mutations causing dilated cardiomyopathy.

Grosch M, Schraft L, Chan A, Küchenhoff L, Rapti K, Ferreira AM, Kornienko J, Li S, Radke MH, Krämer C, Clauder-Münster S, Perlas E, Backs J, Gotthardt M, Dieterich C, van den Hoogenhof MMG, Grimm D, Steinmetz LM

Nature communications, 2023

doi:10.1038/s41467-023-39352-1.

Transcriptional neighborhoods regulate transcript isoform lengths and expression levels.

Brooks AN, Hughes AL, Clauder-Münster S, Mitchell LA, Boeke JD, Steinmetz LM

Science (New York, N.Y.), 2022

doi:10.1126/science.abg0162.

High-speed fluorescence image-enabled cell sorting.

Schraivogel D, Kuhn TM, Rauscher B, Rodríguez-Martínez M, Paulsen M, Owsley K, Middlebrook A, Tischer C, Ramasz B, Ordoñez-Rueda D, Dees M, Cuylen-Haering S, Diebold E, Steinmetz LM

Science (New York, N.Y.), 2022

doi:10.1126/science.abj3013.

Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms in cardiomyocytes.

Zhu C, Wu J, Sun H, Briganti F, Meder B, Wei W, Steinmetz LM

Nature communications, 2021

doi:10.1038/s41467-021-24484-z.

Targeted Perturb-seq enables genome-scale genetic screens in single cells.

Schraivogel D, Gschwind AR, Milbank JH, Leonce DR, Jakob P, Mathur L, Korbel JO, Merten CA, Velten L, Steinmetz LM

Nature methods, 2020

doi:10.1038/s41592-020-0837-5.

Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization.

Baccin C, Al-Sabah J, Velten L, Helbling PM, Grünschläger F, Hernández-Malmierca P, Nombela-Arrieta C, Steinmetz LM, Trumpp A, Haas S

Nature cell biology, 2020

doi:10.1038/s41556-019-0439-6.

Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos.

Zuo E, Sun Y, Wei W, Yuan T, Ying W, Sun H, Yuan L, Steinmetz LM, Li Y, Yang H

Science (New York, N.Y.), 2019

doi:10.1126/science.aav9973.

Multiplexed precision genome editing with trackable genomic barcodes in yeast.

Roy KR, Smith JD, Vonesch SC, Lin G, Tu CS, Lederer AR, Chu A, Suresh S, Nguyen M, Horecka J, Tripathi A, Burnett WT, Morgan MA, Schulz J, Orsley KM, Wei W, Aiyar RS, Davis RW, Bankaitis VA, Haber JE, Salit ML, St Onge RP, Steinmetz LM

Nature biotechnology, 2018

doi:10.1038/nbt.4137.

Human haematopoietic stem cell lineage commitment is a continuous process.

Velten L, Haas SF, Raffel S, Blaszkiewicz S, Islam S, Hennig BP, Hirche C, Lutz C, Buss EC, Nowak D, Boch T, Hofmann WK, Ho AD, Huber W, Trumpp A, Essers MA, Steinmetz LM

Nature cell biology, 2017

doi:10.1038/ncb3493.

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics.

Pelechano V, Wei W, Steinmetz LM

Cell, 2015

doi:10.1016/j.cell.2015.05.008.

Extensive transcriptional heterogeneity revealed by isoform profiling

Pelechano V, Wei W, Steinmetz LM

Nature, 2013

doi:10.1038/nature12121.

The genomic and transcriptomic landscape of a HeLa cell line

Landry JJ, Pyl PT, Rausch T, Zichner T, Tekkedil MM, Stütz AM, Jauch A, Aiyar RS, Pau G, Delhomme N, Gagneur J, Korbel JO, Huber W, Steinmetz LM

G3 (Bethesda, Md.), 2013

doi:10.1534/g3.113.005777.

Dissecting the genetic basis of resistance to malaria parasites in Anopheles gambiae

Blandin SA, Wang-Sattler R, Lamacchia M, Gagneur J, Lycett G, Ning Y, Levashina EA, Steinmetz LM

Science (New York, N.Y.), 2009

doi:10.1126/science.1175241.

Bidirectional promoters generate pervasive transcription in yeast

Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Münster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz LM

Nature, 2009

doi:10.1038/nature07728.

High-resolution mapping of meiotic crossovers and non-crossovers in yeast

Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM

Nature, 2008

doi:10.1038/nature07135.

A high-resolution map of transcription in the yeast genome

David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW, Steinmetz LM

Proceedings of the National Academy of Sciences of the United States of America, 2006

doi:10.1073/pnas.0601091103.

Dissecting the architecture of a quantitative trait locus in yeast

Steinmetz LM, Sinha H, Richards DR, Spiegelman JI, Oefner PJ, McCusker JH, Davis RW

Nature, 2002

doi:10.1038/416326a.

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