Publications – Steinmetz Group

Ehf and Fezf2 regulate late medullary thymic epithelial cell and thymic tuft cell development.

Lammers S, Barrera V, Brennecke P, Miller C, Yoon J, Balolong J, Anderson MS, Ho Sui S, Steinmetz LM, von Andrian UH, Rattay K

Frontiers in immunology, 2023

doi:10.3389/fimmu.2023.1277365.

Size-exclusion chromatography combined with DIA-MS enables deep proteome profiling of extracellular vesicles from melanoma plasma and serum.

Lattmann E, Räss L, Tognetti M, Gómez JMM, Lapaire V, Bruderer R, Reiter L, Feng Y, Steinmetz LM, Levesque MP

Cellular and molecular life sciences : CMLS, 2024

doi:10.1007/s00018-024-05137-y.

Dissecting quantitative trait nucleotides by saturation genome editing.

Roy KR, Smith JD, Li S, Vonesch SC, Nguyen M, Burnett WT, Orsley KM, Lee C, Haber JE, St.Onge RP, Steinmetz LM

bioRxiv, 2024

doi:10.1101/2024.02.02.577784.

Uterine injury during diestrus leads to placental and embryonic defects in future pregnancies in mice.

Zhang ET, Wells KL, Bergman AJ, Ryan EE, Steinmetz LM, Baker JC

Biology of reproduction, 2024

doi:10.1093/biolre/ioae001.

An encyclopedia of enhancer-gene regulatory interactions in the human genome.

Gschwind AR, Mualim KS, Karbalayghareh A, Sheth MU, Dey KK, Jagoda E, Nurtdinov RN, Xi W, Tan AS, Jones H, Ma XR, Yao D, Nasser J, Avsec Ž, James BT, Shamim MS, Durand NC, Rao SSP, Mahajan R, Doughty BR, Andreeva K, Ulirsch JC, Fan K, Perez EM, Nguyen TC, Kelley DR, Finucane HK, Moore JE, Weng Z, Kellis M, Bassik MC, Price AL, Beer MA, Guigó R, Stamatoyannopoulos JA, Aiden EL, Greenleaf WJ, Leslie CS, Steinmetz LM, Kundaje A, Engreitz JM

bioRxiv, 2023

doi:10.1101/2023.11.09.563812.

Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast synIX strains.

McCulloch LH, Sambasivam V, Hughes AL, Annaluru N, Ramalingam S, Fanfani V, Lobzaev E, Mitchell LA, Cai J, Build-A-Genome Class, Jiang H, LaCava J, Taylor MS, Bishai WR, Stracquadanio G, Steinmetz LM, Bader JS, Zhang W, Boeke JD, Chandrasegaran S

Cell genomics, 2023

doi:10.1016/j.xgen.2023.100419.

Design, construction, and functional characterization of a tRNA neochromosome in yeast.

Schindler D, Walker RSK, Jiang S, Brooks AN, Wang Y, Müller CA, Cockram C, Luo Y, García A, Schraivogel D, Mozziconacci J, Pena N, Assari M, Sánchez Olmos MDC, Zhao Y, Ballerini A, Blount BA, Cai J, Ogunlana L, Liu W, Jönsson K, Abramczyk D, Garcia-Ruiz E, Turowski TW, Swidah R, Ellis T, Pan T, Antequera F, Shen Y, Nieduszynski CA, Koszul R, Dai J, Steinmetz LM, Boeke JD, Cai Y

Cell, 2023

doi:10.1016/j.cell.2023.10.015.

Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions.

Zhao Y, Coelho C, Hughes AL, Lazar-Stefanita L, Yang S, Brooks AN, Walker RSK, Zhang W, Lauer S, Hernandez C, Cai J, Mitchell LA, Agmon N, Shen Y, Sall J, Fanfani V, Jalan A, Rivera J, Liang FX, Bader JS, Stracquadanio G, Steinmetz LM, Cai Y, Boeke JD

Cell, 2023

doi:10.1016/j.cell.2023.09.025.

Gut barrier defects, intestinal immune hyperactivation and enhanced lipid catabolism drive lethality in NGLY1-deficient Drosophila.

Pandey A, Galeone A, Han SY, Story BA, Consonni G, Mueller WF, Steinmetz LM, Vaccari T, Jafar-Nejad H

Nature communications, 2023

doi:10.1038/s41467-023-40910-w.

Pooled genome-scale CRISPR screens in single cells.

Schraivogel D, Steinmetz LM, Parts L

Annual review of genetics, 2023

doi:10.1146/annurev-genet-072920-013842.

Large scale microfluidic CRISPR screening for increased amylase secretion in yeast.

Johansson SA, Dulermo T, Jann C, Smith JD, Pryszlak A, Pignede G, Schraivogel D, Colavizza D, Desfougères T, Rave C, Farwick A, Merten CA, Roy KR, Wei W, Steinmetz LM

Lab on a chip, 2023

doi:10.1039/d3lc00111c.

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.

Atlas of mRNA translation and decay for bacteria.

Huch S, Nersisyan L, Ropat M, Barrett D, Wu M, Wang J, Valeriano VD, Vardazaryan N, Huerta-Cepas J, Wei W, Du J, Steinmetz LM, Engstrand L, Pelechano V

Nature microbiology, 2023

doi:10.1038/s41564-023-01393-z.

Genome-scale analysis of interactions between genetic perturbations and natural variation.

Hale JJ, Matsui T, Goldstein I, Mullis MN, Roy KR, Ville CN, Miller D, Wang C, Reynolds T, Steinmetz LM, Levy SF, Ehrenreich IM

bioRxiv, 2023

doi:10.1101/2023.05.06.539663.

A scalable, GMP-compatible, autologous organotypic cell therapy for Dystrophic Epidermolysis Bullosa.

Neumayer G, Torkelson JL, Li S, McCarthy K, Zhen HH, Vangipuram M, Jackow J, Rami A, Hansen C, Guo Z, Gaddam S, Pappalardo A, Li L, Cramer A, Roy KR, Nguyen TM, Tanabe K, McGrath PS, Bruckner A, Bilousova G, Roop D, Bailey I, Tang JY, Christiano A, Steinmetz LM, Wernig M, Oro AE

bioRxiv, 2023

doi:10.1101/2023.02.28.529447.

Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation.

Li B, Zeis P, Zhang Y, Alekseenko A, Fürst E, Sanchez YP, Lin G, Tekkedil MM, Piazza I, Steinmetz LM, Pelechano V

Nature communications, 2023

doi:10.1038/s41467-023-36586-x.

Cell sorters see things more clearly now.

Schraivogel D, Steinmetz LM

Molecular systems biology, 2023

doi:10.15252/msb.202211254.

Cardiac splicing as a diagnostic and therapeutic target.

Gotthardt M, Badillo-Lisakowski V, Parikh VN, Ashley E, Furtado M, Carmo-Fonseca M, Schudy S, Meder B, Grosch M, Steinmetz L, Crocini C, Leinwand L

Nature reviews. Cardiology, 2023

doi:10.1038/s41569-022-00828-0.

Deep phenotyping of two pre-clinical mouse models and a cohort of RBM20 mutation carriers reveals no sex-dependent disease severity in RBM20 cardiomyopathy.

Lennermann DC, Pepin ME, Grosch M, Konrad L, Kemmling E, Hartmann J, Nolte JL, Clauder-Münster S, Kayvanpour E, Sedaghat-Hamedani F, Haas J, Meder B, van den Boogaard M, Amin AS, Dewenter M, Krüger M, Steinmetz LM, Backs J, van den Hoogenhof MMG

American Journal of Physiology - Heart and Circulatory Physiology, 2022

doi:10.1152/ajpheart.00328.2022.

Transcription factor GATA4 regulates cell type-specific splicing through direct interaction with RNA in human induced pluripotent stem cell-derived cardiac progenitors.

Zhu L, Choudhary K, Gonzalez-Teran B, Ang YS, Thomas R, Stone NR, Liu L, Zhou P, Zhu C, Ruan H, Huang Y, Jin S, Pelonero A, Koback F, Padmanabhan A, Sadagopan N, Hsu A, Costa MW, Gifford CA, van Bemmel J, Hüttenhain R, Vedantham V, Conklin BR, Black BL, Bruneau BG, Steinmetz L, Krogan NJ, Pollard KS, Srivastava D

Circulation, 2022

doi:10.1161/circulationaha.121.057620.

Transcriptomic diversity in human medullary thymic epithelial cells.

Carter JA, Strömich L, Peacey M, Chapin SR, Velten L, Steinmetz LM, Brors B, Pinto S, Meyer HV

Nature communications, 2022

doi:10.1038/s41467-022-31750-1.

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.

KIR + CD8 + T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19.

Li J, Zaslavsky M, Su Y, Guo J, Sikora MJ, van Unen V, Christophersen A, Chiou SH, Chen L, Li J, Ji X, Wilhelmy J, McSween AM, Palanski BA, Mallajosyula VVA, Bracey NA, Dhondalay GKR, Bhamidipati K, Pai J, Kipp LB, Dunn JE, Hauser SL, Oksenberg JR, Satpathy AT, Robinson WH, Dekker CL, Steinmetz LM, Khosla C, Utz PJ, Sollid LM, Chien YH, Heath JR, Fernandez-Becker NQ, Nadeau KC, Saligrama N, Davis MM

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

doi:10.1126/science.abi9591.

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.

Assembly-dependent translation of subunits 6 (Atp6) and 9 (Atp9) of ATP synthase in yeast mitochondria.

Kabala AM, Binko K, Godard F, Charles C, Dautant A, Baranowska E, Skoczen N, Gombeau K, Bouhier M, Becker HD, Ackerman SH, Steinmetz LM, Tribouillard-Tanvier D, Kucharczyk R, di Rago JP

Genetics, 2022

doi:10.1093/genetics/iyac007.

Patient-derived gene and protein expression signatures of NGLY1 deficiency.

Rauscher B, Mueller WF, Clauder-Münster S, Jakob P, Islam MS, Sun H, Ghidelli-Disse S, Boesche M, Bantscheff M, Pflaumer H, Collier P, Haase B, Chen S, Hoffman R, Wang G, Benes V, Drewes G, Snyder M, Steinmetz LM

Journal of biochemistry, 2021

doi:10.1093/jb/mvab131.

High-throughput functional characterization of protein phosphorylation sites in yeast.

Viéitez C, Busby BP, Ochoa D, Mateus A, Memon D, Galardini M, Yildiz U, Trovato M, Jawed A, Geiger AG, Oborská-Oplová M, Potel CM, Vonesch SC, Szu Tu C, Shahraz M, Stein F, Steinmetz LM, Panse VG, Noh KM, Savitski MM, Typas A, Beltrao P

Nature biotechnology, 2021

doi:10.1038/s41587-021-01051-x.

Integrated single-cell transcriptomics and epigenomics reveals strong germinal center-associated etiology of autoimmune risk loci.

King HW, Wells KL, Shipony Z, Kathiria AS, Wagar LE, Lareau C, Orban N, Capasso R, Davis MM, Steinmetz LM, James LK, Greenleaf WJ

Science immunology, 2021

doi:10.1126/sciimmunol.abh3768.

Regulation of Msh4-Msh5 association with meiotic chromosomes in budding yeast.

Nandanan KG, Salim S, Pankajam AV, Shinohara M, Lin G, Chakraborty P, Farnaz A, Steinmetz LM, Shinohara A, Nishant KT

Genetics, 2021

doi:10.1093/genetics/iyab102.

RBM20-related cardiomyopathy: current understanding and future options.

Koelemen J, Gotthardt M, Steinmetz LM, Meder B

Journal of clinical medicine, 2021

doi:10.3390/jcm10184101.

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.

Author correction: dysregulated ribonucleoprotein granules promote cardiomyopathy in RBM20 gene-edited pigs.

Schneider JW, Oommen S, Qureshi MY, Goetsch SC, Pease DR, Sundsbak RS, Guo W, Sun M, Sun H, Kuroyanagi H, Webster DA, Coutts AW, Holst KA, Edwards BS, Newville N, Hathcock MA, Melkamu T, Briganti F, Wei W, Romanelli MG, Fahrenkrug SC, Frantz DE, Olson TM, Steinmetz LM, Carlson DF, Nelson TJ, Wanek Program Preclinical Pipeline

Nature medicine, 2021

doi:10.1038/s41591-021-01412-8.

Single-cell analyses reveal SARS-CoV-2 interference with intrinsic immune response in the human gut.

Triana S, Metz-Zumaran C, Ramirez C, Kee C, Doldan P, Shahraz M, Schraivogel D, Gschwind AR, Sharma AK, Steinmetz LM, Herrmann C, Alexandrov T, Boulant S, Stanifer ML

Molecular systems biology, 2021

doi:10.15252/msb.202110232.

The chaperone-binding activity of the mitochondrial surface receptor Tom70 protects the cytosol against mitoprotein-induced stress.

Backes S, Bykov YS, Flohr T, Räschle M, Zhou J, Lenhard S, Krämer L, Mühlhaus T, Bibi C, Jann C, Smith JD, Steinmetz LM, Rapaport D, Storchová Z, Schuldiner M, Boos F, Herrmann JM

Cell reports, 2021

doi:10.1016/j.celrep.2021.108936.

Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics.

Velten L, Story BA, Hernández-Malmierca P, Raffel S, Leonce DR, Milbank J, Paulsen M, Demir A, Szu-Tu C, Frömel R, Lutz C, Nowak D, Jann JC, Pabst C, Boch T, Hofmann WK, Müller-Tidow C, Trumpp A, Haas S, Steinmetz LM

Nature communications, 2021

doi:10.1038/s41467-021-21650-1.

CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate.

Gutmann F, Jann C, Pereira F, Johansson A, Steinmetz LM, Patil KR

Biotechnology for biofuels, 2021

doi:10.1186/s13068-021-01880-7.

Fast and inexpensive whole-genome sequencing library preparation from intact yeast cells.

Vonesch SC, Li S, Szu Tu C, Hennig BP, Dobrev N, Steinmetz LM

G3 (Bethesda, Md.), 2021

doi:10.1093/g3journal/jkaa009.

A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae.

Rodríguez-Galán O, García-Gómez JJ, Rosado IV, Wei W, Méndez-Godoy A, Pillet B, Alekseenko A, Steinmetz LM, Pelechano V, Kressler D, de la Cruz J

Nucleic acids research, 2020

doi:10.1093/nar/gkaa1200.

Dysregulated ribonucleoprotein granules promote cardiomyopathy in RBM20 gene-edited pigs.

Schneider JW, Oommen S, Qureshi MY, Goetsch SC, Pease DR, Sundsbak RS, Guo W, Sun M, Sun H, Kuroyanagi H, Webster DA, Coutts AW, Holst KA, Edwards BS, Newville N, Hathcock MA, Melkamu T, Briganti F, Wei W, Romanelli MG, Fahrenkrug SC, Frantz DE, Olson TM, Steinmetz LM, Carlson DF, Nelson TJ, Wanek Program Preclinical Pipeline

Nature medicine, 2020

doi:10.1038/s41591-020-1087-x.

Combined transient ablation and single cell RNA sequencing reveals the development of medullary thymic epithelial cells.

Wells KL, Miller CN, Gschwind AR, Wei W, Phipps JD, Anderson MS, Steinmetz LM

eLife, 2020

doi:10.7554/eLife.60188.

Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.

Garrido-Godino AI, Gupta I, Gutiérrez-Santiago F, Martínez-Padilla AB, Alekseenko A, Steinmetz LM, Pérez-Ortín JE, Pelechano V, Navarro F

RNA biology, 2020

doi:10.1080/15476286.2020.1839229.

iPSC modeling of RBM20-deficient DCM identifies upregulation of RBM20 as a therapeutic strategy.

Briganti F, Sun H, Wei W, Wu J, Zhu C, Liss M, Karakikes I, Rego S, Cipriano A, Snyder M, Meder B, Xu Z, Millat G, Gotthardt M, Mercola M, Steinmetz LM

Cell reports, 2020

doi:10.1016/j.celrep.2020.108117.

TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes.

Wang J, Li B, Marques S, Steinmetz LM, Wei W, Pelechano V

Nucleic acids research, 2020

doi:10.1093/nar/gkaa691.

GOTI, a method to identify genome-wide off-target effects of genome editing in mouse embryos.

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

Nature protocols, 2020

doi:10.1038/s41596-020-0361-1.

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.

McQ – an open-source multiplexed SARS-CoV-2 quantification platform.

Vonesch SC, Bredikhin D, Dobrev N, Villacorta L, Kleinendorst R, Cacace E, Flock J, Frank M, Jung F, Kornienko J, Mitosch K, Osuna-Lopez M, Zimmermann J, Goettig S, Hamprecht A, Kraeusslich H, Knop M, Typas A, Steinmetz LM, Benes V, Remans K, Krebs AR

medRxiv, 2020

doi:10.1101/2020.12.02.20242628.

Loss of N-glycanase 1 alters transcriptional and translational regulation in K562 cell lines.

Mueller WF, Jakob P, Sun H, Clauder-Münster S, Ghidelli-Disse S, Ordonez D, Boesche M, Bantscheff M, Collier P, Haase B, Benes V, Paulsen M, Sehr P, Lewis J, Drewes G, Steinmetz LM

G3 (Bethesda, Md.), 2020

doi:10.1534/g3.119.401031.

A circulating bioreactor reprograms cancer cells toward a more mesenchymal niche.

Calamak S, Ermis M, Sun H, Islam S, Sikora M, Nguyen M, Hasirci V, Steinmetz LM, Demirci U

Advanced biosystems, 2020

doi:10.1002/adbi.201900139.

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, 2019

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

Towards a systematic map of the functional role of protein phosphorylation.

Viéitez C, Busby BP, Ochoa D, Mateus A, Galardini M, Jawed A, Memon D, Potel CM, Vonesch SC, Tu CS, Shahraz M, Stein F, Steinmetz LM, Savitski MM, Typas A, Beltrao P

bioRxiv, 2019

doi:10.1101/872770.

Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast.

Wei W, Hennig BP, Wang J, Zhang Y, Piazza I, Pareja Sanchez Y, Chabbert CD, Adjalley SH, Steinmetz LM, Pelechano V

Genome research, 2019

doi:10.1101/gr.243378.118.

Liver-specific deletion of Ngly1 causes abnormal nuclear morphology and lipid metabolism under food stress.

Fujihira H, Masahara-Negishi Y, Akimoto Y, Hirayama H, Lee HC, Story BA, Mueller WF, Jakob P, Clauder-Münster S, Steinmetz LM, Radhakrishnan SK, Kawakami H, Kamada Y, Miyoshi E, Yokomizo T, Suzuki T

Biochimica et biophysica acta. Molecular basis of disease, 2019

doi:10.1016/j.bbadis.2019.165588.

Biological plasticity rescues target activity in CRISPR knock outs.

Smits AH, Ziebell F, Joberty G, Zinn N, Mueller WF, Clauder-Münster S, Eberhard D, Fälth Savitski M, Grandi P, Jakob P, Michon AM, Sun H, Tessmer K, Bürckstümmer T, Bantscheff M, Drewes G, Steinmetz LM, Huber W

Nature methods, 2019

doi:10.1038/s41592-019-0614-5.

Yeast single-cell RNA-seq, cell by cell and step by step.

Nadal-Ribelles M, Islam S, Wei W, Latorre P, Nguyen M, de Nadal E, Posas F, Steinmetz LM

BIO-PROTOCOL, 2019

doi:10.21769/BioProtoc.3359.

Opposing T cell responses in experimental autoimmune encephalomyelitis.

Saligrama N, Zhao F, Sikora MJ, Serratelli WS, Fernandes RA, Louis DM, Yao W, Ji X, Idoyaga J, Mahajan VB, Steinmetz LM, Chien YH, Hauser SL, Oksenberg JR, Garcia KC, Davis MM

Nature, 2019

doi:10.1038/s41586-019-1467-x.

Select sequencing of clonally expanded CD8+ T cells reveals limits to clonal expansion.

Huang H, Sikora MJ, Islam S, Chowdhury RR, Chien YH, Scriba TJ, Davis MM, Steinmetz LM

Proceedings of the National Academy of Sciences of the United States of America, 2019

doi:10.1073/pnas.1902649116.

Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations.

Nadal-Ribelles M, Islam S, Wei W, Latorre P, Nguyen M, de Nadal E, Posas F, Steinmetz LM

Nature microbiology, 2019

doi:10.1038/s41564-018-0346-9.

Evolthon: a community endeavor to evolve lab evolution.

Kaminski Strauss S, Schirman D, Jona G, Brooks AN, Kunjapur AM, Nguyen Ba AN, Flint A, Solt A, Mershin A, Dixit A, Yona AH, Csörgő B, Busby BP, Hennig BP, Pál C, Schultz D, Schraivogel D, Agashe D, Wernick DG, Zabezhinsky D, Levi D, Sass E, Russ D, Herz E, Tamar E, Church GM, Levy ED, Nachman I, Yelin I, Georgeson JM, Gerst JE, Rübsam M, Ralser M, Adamala KP, Steinmetz LM, Walunjkar N, Yin N, Klutstein M, Desai MM, Snitser O, Adini O, Aharon Hefetz N, Jakimo N, Zeidan R, Hazan R, Kumar P, Soo Hoo Smith R, Nouriel S, Johnson S, Kishony R, Rak R, Wein T, Dagan T, Foster S, Vonesch SC, Olin-Sandoval V, Mueller WF, Stiles T, Wannier TM, Karydis T, Pilpel Y, Dahan O, Bar-On YM

PLoS biology, 2019

doi:10.1371/journal.pbio.3000182.

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.

High-frequency actionable pathogenic exome variants in an average-risk cohort.

Rego S, Dagan-Rosenfeld O, Zhou W, Sailani MR, Limcaoco P, Colbert E, Avina M, Wheeler J, Craig C, Salins D, Röst HL, Dunn J, McLaughlin T, Steinmetz LM, Bernstein JA, Snyder MP

Cold Spring Harbor molecular case studies, 2018

doi:10.1101/mcs.a003178.

Conventional and neo-antigenic peptides presented by β cells are targeted by circulating naïve CD8+ T Cells in type 1 diabetic and health donors.

Gonzalez-Duque S, Azoury ME, Colli ML, Afonso G, Turatsinze JV, Nigi L, Lalanne AI, Sebastiani G, Carré A, Pinto S, Culina S, Corcos N, Bugliani M, Marchetti P, Armanet M, Kyewski B, Diedisheim M, Buus S, Steinmetz LM, Dubois-Laforgue D, You S, Beressi JP, Larger E, Dotta F, Bruno G, Eizirik DL, Scharfmann R, Vinh J, Verdier Y, Mallone R

Cell metabolism, 2018

doi:10.1016/j.cmet.2018.07.007.

Gain of CTCF-anchored chromatin loops marks the exit from naive pluripotency.

Pękowska A, Klaus B, Xiang W, Severino J, Daigle N, Klein FA, Oleś M, Casellas R, Ellenberg J, Steinmetz LM, Bertone P, Huber W

Cell systems, 2018

doi:10.1016/j.cels.2018.09.003.

NAD(P)HX repair deficiency causes central metabolic perturbations in yeast and human cells.

Becker-Kettern J, Paczia N, Conrotte JF, Zhu C, Fiehn O, Jung PP, Steinmetz LM, Linster CL

The FEBS journal, 2018

doi:10.1111/febs.14631.

Condensin controls cellular RNA levels through the accurate segregation of chromosomes instead of directly regulating transcription

Hocquet C, Robellet X, Modolo L, Sun X-M, Burny C, Cuylen-Haering S, Toselli E, Clauder-Munster S, Steinmetz L, Haering CH, Marguerat S, Bernard P

2018

doi:10.7554/eLife.38517.

Rpd3L HDAC links H3K4me3 to transcriptional repression memory.

Lee BB, Choi A, Kim JH, Jun Y, Woo H, Ha SD, Yoon CY, Hwang JT, Steinmetz L, Buratowski S, Lee S, Kim HY, Kim T

Nucleic acids research, 2018

doi:10.1093/nar/gky573.

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.

HEx: A heterologous expression platform for the discovery of fungal natural products.

Harvey CJB, Tang M, Schlecht U, Horecka J, Fischer CR, Lin HC, Li J, Naughton B, Cherry J, Miranda M, Li YF, Chu AM, Hennessy JR, Vandova GA, Inglis D, Aiyar RS, Steinmetz LM, Davis RW, Medema MH, Sattely E, Khosla C, St Onge RP, Tang Y, Hillenmeyer ME

Science advances, 2018

doi:10.1126/sciadv.aar5459.

Large-scale low-cost NGS library preparation using a robust Tn5 purification and tagmentation protocol.

Hennig BP, Velten L, Racke I, Szu Tu C, Thoms M, Rybin V, Besir H, Remans K, Steinmetz LM

G3 (Bethesda, Md.), 2017

doi:10.1534/g3.117.300257.

Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis.

Chabbert CD, Adjalley SH, Steinmetz LM, Pelechano V

Methods in molecular biology (Clifton, N.J.), 2017

doi:10.1007/978-1-4939-7380-4_16.

Inhibition of NGLY1 Inactivates the Transcription Factor Nrf1 and Potentiates Proteasome Inhibitor Cytotoxicity.

Tomlin FM, Gerling-Driessen UIM, Liu YC, Flynn RA, Vangala JR, Lentz CS, Clauder-Muenster S, Jakob P, Mueller WF, Ordoñez-Rueda D, Paulsen M, Matsui N, Foley D, Rafalko A, Suzuki T, Bogyo M, Steinmetz LM, Radhakrishnan SK, Bertozzi CR

ACS central science, 2017

doi:10.1021/acscentsci.7b00224.

Genome Dynamics of Hybrid Saccharomyces cerevisiae During Vegetative and Meiotic Divisions.

Dutta A, Lin G, Pankajam AV, Chakraborty P, Bhat N, Steinmetz LM, Nishant KT

G3 (Bethesda, Md.), 2017

doi:10.1534/g3.117.1135.

A new fate mapping system reveals context-dependent random or clonal expansion of microglia.

Tay TL, Mai D, Dautzenberg J, Fernández-Klett F, Lin G, Sagar G, Datta M, Drougard A, Stempfl T, Ardura-Fabregat A, Staszewski O, Margineanu A, Sporbert A, Steinmetz LM, Pospisilik JA, Jung S, Priller J, Grün D, Ronneberger O, Prinz M

Nature neuroscience, 2017

doi:10.1038/nn.4547.

Modulating Crossover Frequency and Interference for Obligate Crossovers in Saccharomyces cerevisiae Meiosis.

Chakraborty P, Pankajam AV, Lin G, Dutta A, Nandanan KG, Tekkedil MM, Shinohara A, Steinmetz LM, Thazath NK

G3 (Bethesda, Md.), 2017

doi:10.1534/g3.117.040071.

Assembly of functionally integrated human forebrain spheroids.

Birey F, Andersen J, Makinson CD, Islam S, Wei W, Huber N, Fan HC, Metzler KRC, Panagiotakos G, Thom N, O'Rourke NA, Steinmetz LM, Bernstein JA, Hallmayer J, Huguenard JR, Paşca SP

Nature, 2017

doi:10.1038/nature22330.

INO80 represses osmostress induced gene expression by resetting promoter proximal nucleosomes.

Klopf E, Schmidt HA, Clauder-Münster S, Steinmetz LM, Schüller C

Nucleic acids research, 2016

doi:10.1093/nar/gkw1292.

Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates.

Mall M, Kareta MS, Chanda S, Ahlenius H, Perotti N, Zhou B, Grieder SD, Ge X, Drake S, Euong Ang C, Walker BM, Vierbuchen T, Fuentes DR, Brennecke P, Nitta KR, Jolma A, Steinmetz LM, Taipale J, Südhof TC, Wernig M

Nature, 2017

doi:10.1038/nature21722.

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.

A method for high-throughput production of sequence-verified DNA libraries and strain collections.

Smith JD, Schlecht U, Xu W, Suresh S, Horecka J, Proctor MJ, Aiyar RS, Bennett RA, Chu A, Li YF, Roy K, Davis RW, Steinmetz LM, Hyman RW, Levy SF, St Onge RP

Molecular systems biology, 2017

doi:10.15252/msb.20167233.

The State of Systems Genetics in 2017.

Baliga NS, Björkegren JL, Boeke JD, Boutros M, Crawford NP, Dudley AM, Farber CR, Jones A, Levey AI, Lusis AJ, Mak HC, Nadeau JH, Noyes MB, Petretto E, Seyfried NT, Steinmetz LM, Vonesch SC

Cell systems, 2017

doi:10.1016/j.cels.2017.01.005.

Modulation of mRNA and lncRNA expression dynamics by the Set2-Rpd3S pathway.

Kim JH, Lee BB, Oh YM, Zhu C, Steinmetz LM, Lee Y, Kim WK, Lee SB, Buratowski S, Kim T

Nature communications, 2016

doi:10.1038/ncomms13534.

A global genetic interaction network maps a wiring diagram of cellular function.

Costanzo M, VanderSluis B, Koch EN, Baryshnikova A, Pons C, Tan G, Wang W, Usaj M, Hanchard J, Lee SD, Pelechano V, Styles EB, Billmann M, van Leeuwen J, van Dyk N, Lin ZY, Kuzmin E, Nelson J, Piotrowski JS, Srikumar T, Bahr S, Chen Y, Deshpande R, Kurat CF, Li SC, Li Z, Usaj MM, Okada H, Pascoe N, San Luis BJ, Sharifpoor S, Shuteriqi E, Simpkins SW, Snider J, Suresh HG, Tan Y, Zhu H, Malod-Dognin N, Janjic V, Przulj N, Troyanskaya OG, Stagljar I, Xia T, Ohya Y, Gingras AC, Raught B, Boutros M, Steinmetz LM, Moore CL, Rosebrock AP, Caudy AA, Myers CL, Andrews B, Boone C

Science (New York, N.Y.), 2016

doi:10.1126/science.aaf1420.

Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters.

Chen Y, Pai AA, Herudek J, Lubas M, Meola N, Järvelin AI, Andersson R, Pelechano V, Steinmetz LM, Jensen TH, Sandelin A

Nature genetics, 2016

doi:10.1038/ng.3616.

Protein Abundance Control by Non-coding Antisense Transcription.

Huber F, Bunina D, Gupta I, Khmelinskii A, Meurer M, Theer P, Steinmetz LM, Knop M

Cell reports, 2016

doi:10.1016/j.celrep.2016.05.043.

Meiotic Interactors of a Mitotic Gene TAO3 Revealed by Functional Analysis of its Rare Variant.

Gupta S, Radhakrishnan A, Nitin R, Raharja-Liu P, Lin G, Steinmetz LM, Gagneur J, Sinha H

G3 (Bethesda, Md.), 2016

doi:10.1534/g3.116.029900.

Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation

Chlamydas S, Holz H, Samata M, Chelmicki T, Georgiev P, Pelechano V, Dundar F, Dasmeh P, Mittler G, Cadete FT, Ramirez F, Conrad T, Wei W, Raja S, Manke T, Luscombe NM, Steinmetz LM, Akhtar A

NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2016

doi:10.1038/nsmb.3233.

Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex.

Gupta I, Villanyi Z, Kassem S, Hughes C, Panasenko OO, Steinmetz LM, Collart MA

Cell reports, 2016

doi:10.1016/j.celrep.2016.04.055.

The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons

Garcia-Martinez J, Delgado-Ramos L, Ayala G, Pelechano V, Medina DA, Carrasco F, Gonzalez R, Andres-Leon E, Steinmetz L, Warringer J, Chavez S, Perez-Ortin JE

Nucleic acids research, 2016

doi:10.1093/nar/gkv1512.

DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies.

Chabbert CD, Steinmetz LM, Klaus B

PeerJ, 2016

doi:10.7717/peerj.1981.

Sensing a revolution.

Lars M. Steinmetz & Allan Jones

2016

doi:10.15252/msb.20166873.

Landscape and Dynamics of Transcription Initiation in the Malaria Parasite Plasmodium falciparum.

Adjalley SH, Chabbert CD, Klaus B, Pelechano V, Steinmetz LM

Cell reports, 2016

doi:10.1016/j.celrep.2016.02.025.

Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design.

Smith JD, Suresh S, Schlecht U, Wu M, Wagih O, Peltz G, Davis RW, Steinmetz LM, Parts L, St Onge RP

Genome biology, 2016

doi:10.1186/s13059-016-0900-9.

Genome-wide quantification of 5'-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics.

Pelechano V, Wei W, Steinmetz LM

Nature protocols, 2016

doi:10.1038/nprot.2016.026.

SYGNALing a Red Light for Glioblastoma.

Brooks AN, Mueller WF, Steinmetz LM

2016

doi:10.1016/j.cels.2016.08.002.

Comprehensive Identification of RNA-Binding Proteins by RNA Interactome Capture.

Castello A, Horos R, Strein C, Fischer B, Eichelbaum K, Steinmetz LM, Krijgsveld J, Hentze MW

Methods in molecular biology (Clifton, N.J.), 2016

doi:10.1007/978-1-4939-3067-8_8.

Genome-Wide Identification of Alternative Polyadenylation Events Using 3'T-Fill.

Wilkening S, Pelechano V, Steinmetz LM

Methods in molecular biology (Clifton, N.J.), 2016

doi:10.1007/978-1-4939-3067-8_18.

Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough.

Holmes RK, Tuck AC, Zhu C, Dunn-Davies HR, Kudla G, Clauder-Munster S, Granneman S, Steinmetz LM, Guthrie C, Tollervey D

PLoS genetics, 2015

doi:10.1371/journal.pgen.1005735.

Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis.

Rege M, Subramanian V, Zhu C, Hsieh TH, Weiner A, Friedman N, Clauder-Münster S, Steinmetz LM, Rando OJ, Boyer LA, Peterson CL

Cell reports, 2015

doi:10.1016/j.celrep.2015.10.030.

Inflammation-induced emergency megakaryopoiesis driven by hematopoietic stem cell-like megakaryocyte progenitors.

Haas S, Hansson J, Klimmeck D, Loeffler D, Velten L, Uckelmann H, Wurzer S, Prendergast ÁM, Schnell A, Hexel K, Santarella-Mellwig R, Blaszkiewicz S, Kuck A, Geiger H, Milsom MD, Steinmetz LM, Schroeder T, Trumpp A, Krijgsveld J, Essers MA

Cell stem cell, 2015

doi:10.1016/j.stem.2015.07.007.

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions.

Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, Steinmetz LM, Kundaje A, Snyder M

2015

doi:10.1016/j.cell.2015.07.048.

Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells.

Brennecke P, Reyes A, Pinto S, Rattay K, Nguyen M, Küchler R, Huber W, Kyewski B, Steinmetz LM

Nature Immunology, 2015

doi:10.1038/ni.3246.

The Nuclear PolyA-Binding Protein Nab2p Is Essential for mRNA Production.

Schmid M, Olszewski P, Pelechano V, Gupta I, Steinmetz LM, Jensen TH

Cell reports, 2015

doi:10.1016/j.celrep.2015.06.008.

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics.

Pelechano V, Wei W, Steinmetz LM

Cell, 2015

doi:10.1016/j.cell.2015.05.008.

Single-cell polyadenylation site mapping reveals 3' isoform choice variability.

Velten L, Anders S, Pekowska A, Järvelin AI, Huber W, Pelechano V, Steinmetz LM

Molecular systems biology, 2015

doi:10.15252/msb.20156198.

Temporal expression profiling identifies pathways mediating effect of causal variant on phenotype.

Gupta S, Radhakrishnan A, Raharja-Liu P, Lin G, Steinmetz LM, Gagneur J, Sinha H

PLoS genetics, 2015

doi:10.1371/journal.pgen.1005195.

Yeast as a system for modeling mitochondrial disease mechanisms and discovering therapies

Lasserre JP, Dautant A, Aiyar RS, Kucharczyk R, Glatigny A, Tribouillard-Tanvier D, Rytka J, Blondel M, Skoczen N, Reynier P, Pitayu L, Rotig A, Delahodde A, Steinmetz LM, Dujardin G, Procaccio V, di Rago JP

DISEASE MODELS & MECHANISMS, 2015

doi:10.1242/dmm.020438.

Negative feedback buffers effects of regulatory variants.

Bader DM, Wilkening S, Lin G, Tekkedil MM, Dietrich K, Steinmetz LM, Gagneur J

Molecular systems biology, 2015

doi:10.15252/msb.20145844.

A high-throughput ChIP-Seq for large-scale chromatin studies.

Chabbert CD, Adjalley SH, Klaus B, Fritsch ES, Gupta I, Pelechano V, Steinmetz LM

Molecular systems biology, 2015

doi:10.15252/msb.20145776.

Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle.

Jordán-Pla A, Gupta I, de Miguel-Jiménez L, Steinmetz LM, Chávez S, Pelechano V, Pérez-Ortín JE

Nucleic acids research, 2014

doi:10.1093/nar/gku1349.

The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development.

Lardenois A, Stuparevic I, Liu Y, Law MJ, Becker E, Smagulova F, Waern K, Guilleux MH, Horecka J, Chu A, Kervarrec C, Strich R, Snyder M, Davis RW, Steinmetz LM, Primig M

Nucleic acids research, 2014

doi:10.1093/nar/gku1185.

Mitochondrial protein sorting as a therapeutic target for ATP synthase disorders.

Aiyar RS, Bohnert M, Duvezin-Caubet S, Voisset C, Gagneur J, Fritsch ES, Couplan E, von der Malsburg K, Funaya C, Soubigou F, Courtin F, Suresh S, Kucharczyk R, Evrard J, Antony C, St Onge RP, Blondel M, di Rago JP, van der Laan M, Steinmetz LM

Nature Communications, 2014

doi:10.1038/ncomms6585.

Expression of Nuclear and Mitochondrial Genes Encoding ATP Synthase Is Synchronized by Disassembly of a Multisynthetase Complex.

Frechin M, Enkler L, Tetaud E, Laporte D, Senger B, Blancard C, Hammann P, Bader G, Clauder-Münster S, Steinmetz LM, Martin RP, di Rago JP, Becker HD

Molecular cell, 2014

doi:10.1016/j.molcel.2014.10.015.

Roadblock termination by reb1p restricts cryptic and readthrough transcription.

Colin J, Candelli T, Porrua O, Boulay J, Zhu C, Lacroute F, Steinmetz LM, Libri D

Molecular cell, 2014

doi:10.1016/j.molcel.2014.10.026.

Variation in Crossover Frequencies Perturb Crossover Assurance Without Affecting Meiotic Chromosome Segregation in Saccharomyces cerevisiae.

Krishnaprasad GN, Anand MT, Lin G, Tekkedil MM, Steinmetz LM, Nishant KT

Genetics, 2014

doi:10.1534/genetics.114.172320.

Transcription mediated insulation and interference direct gene cluster expression switches.

Nguyen T, Fischl H, Howe FS, Woloszczuk R, Serra Barros A, Xu Z, Brown D, Murray SC, Haenni S, Halstead JM, O'Connor L, Shipkovenska G, Steinmetz LM, Mellor J

eLife, 2014

doi:10.7554/elife.03635.

Ultrasensitive proteome analysis using paramagnetic bead technology.

Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J

Molecular systems biology, 2014

doi:10.15252/msb.20145625.

Induced Mutations in Yeast Cell Populations Adapting to an Unforeseen Challenge.

Moore LS, Wei W, Stolovicki E, Benbenishty T, Wilkening S, Steinmetz LM, Braun E, David L

PloS one, 2014

doi:10.1371/journal.pone.0111133.

The Not5 Subunit of the Ccr4-Not Complex Connects Transcription and Translation.

Villanyi Z, Ribaud V, Kassem S, Panasenko OO, Pahi Z, Gupta I, Steinmetz L, Boros I, Collart MA

PLoS genetics, 2014

doi:10.1371/journal.pgen.1004569.

A Genome-Wide Map of Mitochondrial DNA Recombination in Yeast

Fritsch ES, Chabbert CD, Klaus B, Steinmetz LM

Genetics, 2014

doi:10.1534/genetics.114.166637.

Heritability and genetic basis of protein level variation in an outbred population.

Parts L, Liu YC, Tekkedil M, Steinmetz LM, Caudy AA, Fraser AG, Boone C, Andrews BJ, Rosebrock AP

Genome research, 2014

doi:10.1101/gr.170506.113.

Genome-wide identification of transcript start and end sites by transcript isoform sequencing

Pelechano V, Wei W, Jakob P, Steinmetz LM

Nature protocols, 2014

doi:10.1038/nprot.2014.121.

Yeast Growth Plasticity Is Regulated by Environment-Specific Multi-QTL Interactions

Bhatia A, Yadav A, Gagneur J, Zhu C, Steinmetz LM, Bhanot G, Sinha H

G3 (Bethesda, Md.), 2014

doi:10.1534/g3.113.009142.

Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast.

Castelnuovo M, Zaugg JB, Guffanti E, Maffioletti A, Camblong J, Xu Z, Clauder-Münster S, Steinmetz LM, Luscombe NM, Stutz F

Nucleic acids research, 2014

doi:10.1093/nar/gku100.

An evaluation of high-throughput approaches to QTL mapping in Saccharomyces cerevisiae

Wilkening S, Lin G, Fritsch ES, Tekkedil MM, Anders S, Kuehn R, Nguyen M, Aiyar RS, Proctor M, Sakhanenko NA, Galas DJ, Gagneur J, Deutschbauer A, Steinmetz LM

Genetics, 2014

doi:10.1534/genetics.113.160291.

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions

Gupta I, Clauder-Münster S, Klaus B, Järvelin AI, Aiyar RS, Benes V, Wilkening S, Huber W, Pelechano V, Steinmetz LM

Molecular systems biology, 2014

doi:10.1002/msb.135068.

Control of Cdc28 CDK1 by a stress-induced lncRNA

Nadal-Ribelles M, Solé C, Xu Z, Steinmetz LM, de Nadal E, Posas F

Molecular cell, 2014

doi:10.1016/j.molcel.2014.01.006.

Gene regulation by antisense transcription

Pelechano V, Steinmetz LM

Nature reviews. Genetics, 2013

doi:10.1038/nrg3594.

Extensive variation in chromatin states across humans

Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M

Science (New York, N.Y.), 2013

doi:10.1126/science.1242510.

Drift and conservation of differential exon usage across tissues in primate species

Reyes A, Anders S, Weatheritt RJ, Gibson TJ, Steinmetz LM, Huber W

Proceedings of the National Academy of Sciences of the United States of America, 2013

doi:10.1073/pnas.1307202110.

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.

Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality

Ntini E, Järvelin AI, Bornholdt J, Chen Y, Boyd M, Jørgensen M, Andersson R, Hoof I, Schein A, Andersen PR, Andersen PK, Preker P, Valen E, Zhao X, Pelechano V, Steinmetz LM, Sandelin A, Jensen TH

Nature structural & molecular biology, 2013

doi:10.1038/nsmb.2640.

Multiple genomic changes associated with reorganization of gene regulation and adaptation in yeast

David L, Ben-Harosh Y, Stolovicki E, Moore LS, Nguyen M, Tamse R, Dean J, Mancera E, Steinmetz LM, Braun E

Molecular biology and evolution, 2013

doi:10.1093/molbev/mst071.

An efficient method for genome-wide polyadenylation site mapping and RNA quantification (vol 41, pg e65, 2013)

Wilkening S, Pelechano V, Jarvelin AI, Tekkedil MM, Anders S, Benes V, Steinmetz LM

NUCLEIC ACIDS RESEARCH, 2013

doi:10.1093/nar/gkt364.

Extensive transcriptional heterogeneity revealed by isoform profiling

Pelechano V, Wei W, Steinmetz LM

Nature, 2013

doi:10.1038/nature12121.

System-wide identification of RNA-binding proteins by interactome capture

Castello A, Horos R, Strein C, Fischer B, Eichelbaum K, Steinmetz LM, Krijgsveld J, Hentze MW

Nature protocols, 2013

doi:10.1038/nprot.2013.020.

An efficient method for genome-wide polyadenylation site mapping and RNA quantification

Wilkening S, Pelechano V, Järvelin AI, Tekkedil MM, Anders S, Benes V, Steinmetz LM

Nucleic acids research, 2013

doi:10.1093/nar/gks1249.

Mutated SF3B1 is associated with transcript isoform changes of the genes UQCC and RPL31 both in CLLs and uveal melanomas

Reyes A, Blume Carolin, Pelechano V, Jakob P, Steinmetz LM, Zenz T, Huber W

2013

doi:http://dx.doi.org/10.1101/000992.

Natural sequence variants of yeast environmental sensors confer cell-to-cell expression variability

Fehrmann S, Bottin-Duplus H, Leonidou A, Mollereau E, Barthelaix A, Wei W, Steinmetz LM, Yvert G

Molecular systems biology, 2013

doi:10.1038/msb.2013.53.

Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype

Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, Schuon AK, Pe'er D, Steinmetz LM

PLoS genetics, 2013

doi:10.1371/journal.pgen.1003803.

Silencing of genes and alleles by RNAi in Anopheles gambiae

Lamacchia M, Clayton JR, Wang-Sattler R, Steinmetz LM, Levashina EA, Blandin SA

Methods in molecular biology (Clifton, N.J.), 2013

doi:10.1007/978-1-62703-026-7_11.

The role of Ctk1 kinase in termination of small non-coding RNAs

Lenstra TL, Tudek A, Clauder S, Xu Z, Pachis ST, van Leenen D, Kemmeren P, Steinmetz LM, Libri D, Holstege FC

PloS one, 2013

doi:10.1371/journal.pone.0080495.

Genotyping 1000 yeast strains by next-generation sequencing

Wilkening S, Tekkedil MM, Lin G, Fritsch ES, Wei W, Gagneur J, Lazinski DW, Camilli A, Steinmetz LM

BMC genomics, 2013

doi:10.1186/1471-2164-14-90.

Extensive degradation of RNA precursors by the exosome in wild-type cells

Gudipati RK, Xu Z, Lebreton A, Séraphin B, Steinmetz LM, Jacquier A, Libri D

Molecular cell, 2012

doi:10.1016/j.molcel.2012.08.018.

RNA polymerase II collision interrupts convergent transcription

Hobson DJ, Wei W, Steinmetz LM, Svejstrup JQ

Molecular cell, 2012

doi:10.1016/j.molcel.2012.08.027.

Gene loops enhance transcriptional directionality

Tan-Wong SM, Zaugg JB, Camblong J, Xu Z, Zhang DW, Mischo HE, Ansari AZ, Luscombe NM, Steinmetz LM, Proudfoot NJ

Science (New York, N.Y.), 2012

doi:10.1126/science.1224350.

easyRNASeq: a bioconductor package for processing RNA-Seq data

Delhomme N, Padioleau I, Furlong EE, Steinmetz LM

Bioinformatics (Oxford, England), 2012

doi:10.1093/bioinformatics/bts477.

Genetic modifiers of chromatin acetylation antagonize the reprogramming of epi-polymorphisms

Abraham AL, Nagarajan M, Veyrieras JB, Bottin H, Steinmetz LM, Yvert G

PLoS genetics, 2012

doi:10.1371/journal.pgen.1002958.

Set3 HDAC mediates effects of overlapping noncoding transcription on gene induction kinetics

Kim T, Xu Z, Clauder-Münster S, Steinmetz LM, Buratowski S

Cell, 2012

doi:10.1016/j.cell.2012.08.016.

Rrp6p controls mRNA poly(A) tail length and its decoration with poly(A) binding proteins

Schmid M, Poulsen MB, Olszewski P, Pelechano V, Saguez C, Gupta I, Steinmetz LM, Moore C, Jensen TH

Molecular cell, 2012

doi:10.1016/j.molcel.2012.05.005.

Insights into RNA biology from an atlas of mammalian mRNA-binding proteins.

Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM, Krijgsveld J, Hentze MW

Cell, 2012

doi:10.1016/j.cell.2012.04.031.

Experimental relocation of the mitochondrial ATP9 gene to the nucleus reveals forces underlying mitochondrial genome evolution

Bietenhader M, Martos A, Tetaud E, Aiyar RS, Sellem CH, Kucharczyk R, Clauder-Münster S, Giraud MF, Godard F, Salin B, Sagot I, Gagneur J, Déquard-Chablat M, Contamine V, Hermann-Le Denmat S, Sainsard-Chanet A, Steinmetz LM, di Rago JP

PLoS genetics, 2012

doi:10.1371/journal.pgen.1002876.

Genome-wide H4 K16 acetylation by SAS-I is deposited independently of transcription and histone exchange

Heise F, Chung HR, Weber JM, Xu Z, Klein-Hitpass L, Steinmetz LM, Vingron M, Ehrenhofer-Murray AE

Nucleic acids research, 2012

doi:10.1093/nar/gkr649.

Genome-wide polyadenylation site mapping

Pelechano V, Wilkening S, Järvelin AI, Tekkedil MM, Steinmetz LM

Methods in enzymology, 2012

doi:10.1016/b978-0-12-391938-0.00012-4.

Accumulation of noncoding RNA due to an RNase P defect in Saccharomyces cerevisiae

Marvin MC, Clauder-Münster S, Walker SC, Sarkeshik A, Yates JR 3rd, Steinmetz LM, Engelke DR

RNA (New York, N.Y.), 2011

doi:10.1261/rna.2737511.

A yeast-based assay identifies drugs active against human mitochondrial disorders

Couplan E, Aiyar RS, Kucharczyk R, Kabala A, Ezkurdia N, Gagneur J, St Onge RP, Salin B, Soubigou F, Le Cann M, Steinmetz LM, di Rago JP, Blondel M

Proceedings of the National Academy of Sciences of the United States of America, 2011

doi:10.1073/pnas.1101478108.

Functional consequences of bidirectional promoters

Wei W, Pelechano V, Järvelin AI, Steinmetz LM

Trends in genetics : TIG, 2011

doi:10.1016/j.tig.2011.04.002.

Antisense expression increases gene expression variability and locus interdependency

Xu Z, Wei W, Gagneur J, Clauder-Münster S, Smolik M, Huber W, Steinmetz LM

Molecular systems biology, 2011

doi:10.1038/msb.2011.1.

Genome-wide transcriptome analysis in yeast using high-density tiling arrays

David L, Clauder-Münster S, Steinmetz LM

Methods in molecular biology (Clifton, N.J.), 2011

doi:10.1007/978-1-61779-173-4_7.

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6

Lardenois A, Liu Y, Walther T, Chalmel F, Evrard B, Granovskaia M, Chu A, Davis RW, Steinmetz LM, Primig M

Proceedings of the National Academy of Sciences of the United States of America, 2011

doi:10.1073/pnas.1016459108.

Genome-wide survey of post-meiotic segregation during yeast recombination

Mancera E, Bourgon R, Huber W, Steinmetz LM

Genome biology, 2011

doi:10.1186/gb-2011-12-4-r36.

Yeast Sen1 helicase protects the genome from transcription-associated instability

Mischo HE, Gómez-González B, Grzechnik P, Rondón AG, Wei W, Steinmetz L, Aguilera A, Proudfoot NJ

Molecular cell, 2011

doi:10.1016/j.molcel.2010.12.007.

The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis

Nishant KT, Wei W, Mancera E, Argueso JL, Schlattl A, Delhomme N, Ma X, Bustamante CD, Korbel JO, Gu Z, Steinmetz LM, Alani E

PLoS genetics, 2010

doi:10.1371/journal.pgen.1001109.

Natural single-nucleosome epi-polymorphisms in yeast

Nagarajan M, Veyrieras JB, de Dieuleveult M, Bottin H, Fehrmann S, Abraham AL, Croze S, Steinmetz LM, Gidrol X, Yvert G

PLoS genetics, 2010

doi:10.1371/journal.pgen.1000913.

Genetic analysis of variation in transcription factor binding in yeast

Zheng W, Zhao H, Mancera E, Steinmetz LM, Snyder M

Nature, 2010

doi:10.1038/nature08934.

High-resolution transcription atlas of the mitotic cell cycle in budding yeast

Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM

Genome biology, 2010

doi:10.1186/gb-2010-11-3-r24.

Antagonistic changes in sensitivity to antifungal drugs by mutations of an important ABC transporter gene in a fungal pathogen

Guan W, Jiang H, Guo X, Mancera E, Xu L, Li Y, Steinmetz L, Li Y, Gu Z

PloS one, 2010

doi:10.1371/journal.pone.0011309.

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.

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

Camblong J, Beyrouthy N, Guffanti E, Schlaepfer G, Steinmetz LM, Stutz F

Genes & development, 2009

doi:10.1101/gad.522509.

Array-based genotyping in S.cerevisiae using semi-supervised clustering

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

Bioinformatics (Oxford, England), 2009

doi:10.1093/bioinformatics/btp104.

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

Neil H, Malabat C, d'Aubenton-Carafa Y, Xu Z, Steinmetz LM, Jacquier A

Nature, 2009

doi:10.1038/nature07747.

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.

Genome-wide allele- and strand-specific expression profiling

Gagneur J, Sinha H, Perocchi F, Bourgon R, Huber W, Steinmetz LM

Molecular systems biology, 2009

doi:10.1038/msb.2009.31.

Identification of mitochondrial disease genes through integrative analysis of multiple datasets

Aiyar RS, Gagneur J, Steinmetz LM

Methods (San Diego, Calif.), 2008

doi:10.1016/j.ymeth.2008.10.002.

Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast

Sinha H, David L, Pascon RC, Clauder-Münster S, Krishnakumar S, Nguyen M, Shi G, Dean J, Davis RW, Oefner PJ, McCusker JH, Steinmetz LM

Genetics, 2008

doi:10.1534/genetics.108.092932.

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.

Systematic screens for human disease genes, from yeast to human and back

Perocchi F, Mancera E, Steinmetz LM

Molecular bioSystems, 2008

doi:10.1039/b709494a.

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789

Wei W, McCusker JH, Hyman RW, Jones T, Ning Y, Cao Z, Gu Z, Bruno D, Miranda M, Nguyen M, Wilhelmy J, Komp C, Tamse R, Wang X, Jia P, Luedi P, Oefner PJ, David L, Dietrich FS, Li Y, Davis RW, Steinmetz LM

Proceedings of the National Academy of Sciences of the United States of America, 2007

doi:10.1073/pnas.0701291104.

Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D

Perocchi F, Xu Z, Clauder-Münster S, Steinmetz LM

Nucleic acids research, 2007

doi:10.1093/nar/gkm683.

Mosaic genome architecture of the Anopheles gambiae species complex

Wang-Sattler R, Blandin S, Ning Y, Blass C, Dolo G, Touré YT, delle Torre A, Lanzaro GC, Steinmetz LM, Kafatos FC, Zheng L

PloS one, 2007

doi:10.1371/journal.pone.0001249.

Assessing systems properties of yeast mitochondria through an interaction map of the organelle

Perocchi F, Jensen LJ, Gagneur J, Ahting U, von Mering C, Bork P, Prokisch H, Steinmetz LM

PLoS genetics, 2006

doi:10.1371/journal.pgen.0020170.

Capturing cellular machines by systematic screens of protein complexes

Gagneur J, David L, Steinmetz LM

Trends in microbiology, 2006

doi:10.1016/j.tim.2006.06.002.

Transcript mapping with high-density oligonucleotide tiling arrays

Huber W, Toedling J, Steinmetz LM

Bioinformatics (Oxford, England), 2006

doi:10.1093/bioinformatics/btl289.

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.

Complex genetic interactions in a quantitative trait locus

Sinha H, Nicholson BP, Steinmetz LM, McCusker JH

PLoS genetics, 2006

doi:10.1371/journal.pgen.0020013.

Re-analysis of data and its integration

Jensen LJ, Steinmetz LM

FEBS letters, 2005

doi:10.1016/j.febslet.2005.02.006.

Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae

Gu Z, David L, Petrov D, Jones T, Davis RW, Steinmetz LM

Proceedings of the National Academy of Sciences of the United States of America, 2005

doi:10.1073/pnas.0409159102.

Integrative analysis of the mitochondrial proteome in yeast

Prokisch H, Scharfe C, Camp DG 2nd, Xiao W, David L, Andreoli C, Monroe ME, Moore RJ, Gritsenko MA, Kozany C, Hixson KK, Mottaz HM, Zischka H, Ueffing M, Herman ZS, Davis RW, Meitinger T, Oefner PJ, Smith RD, Steinmetz LM

PLoS biology, 2004

doi:10.1371/journal.pbio.0020160.