Guckelberger P; Doughty BR; Munson G; Rao SSP; Tan Y; Cai XS; Fulco CP; Nasser J; Mualim KS; Bergman DT; Ray J; Jagoda E; Munger CJ; Gschwind AR; Sheth MU; Tan AS; Pulido SG; Mitra N; Weisz D; Shamim MS; Durand NC; Mahajan R; Khan R; Steinmetz LM; Kanemaki MT; Lander ES; Meissner A; Aiden EL; Engreitz JM, 2024. Cohesin-mediated 3D contacts tune enhancer-promoter regulation. bioRxiv.
Neumayer G; Torkelson JL; Li S; McCarthy K; Zhen HH; Vangipuram M; Mader MM; Gebeyehu G; Jaouni TM; Jacków-Malinowska J; Rami A; Hansen C; Guo Z; Gaddam S; Tate KM; Pappalardo A; Li L; Chow GM; Roy KR; Nguyen TM; Tanabe K; McGrath PS; Cramer A; Bruckner A; Bilousova G; Roop D; Tang JY; Christiano A; Steinmetz LM; Wernig M; Oro AE, 2024. A scalable and cGMP-compatible autologous organotypic cell therapy for Dystrophic Epidermolysis Bullosa. Nat Commun 15(1):5834
Mall M; Kareta MS; Chanda S; Ahlenius H; Perotti N; Zhou B; Grieder SD; Ge X; Drake S; Ang CE; Walker BM; Vierbuchen T; Fuentes DR; Brennecke P; Nitta KR; Jolma A; Steinmetz LM; Taipale J; Südhof TC; Wernig M, 2024. Author Correction: Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates. Nature 630(8017):E11
Lin WH; Opoc FJG; Liao CW; Roy KR; Steinmetz LM; Leu JY, 2024. Histone deacetylase Hos2 regulates protein expression noise by potentially modulating the protein translation machinery. Nucleic Acids Res 52(13):7556-7571
Hale JJ; Matsui T; Goldstein I; Mullis MN; Roy KR; Ville CN; Miller D; Wang C; Reynolds T; Steinmetz LM; Levy SF; Ehrenreich IM, 2024. Genome-scale analysis of interactions between genetic perturbations and natural variation. Nat Commun 15(1):4234
Lammers S; Barrera V; Brennecke P; Miller C; Yoon J; Balolong J; Anderson MS; Ho Sui S; Steinmetz LM; von Andrian UH; Rattay K, 2023. Ehf and Fezf2 regulate late medullary thymic epithelial cell and thymic tuft cell development. Front Immunol 14:1277365
Lattmann E; Räss L; Tognetti M; Gómez JMM; Lapaire V; Bruderer R; Reiter L; Feng Y; Steinmetz LM; Levesque MP, 2024. Size-exclusion chromatography combined with DIA-MS enables deep proteome profiling of extracellular vesicles from melanoma plasma and serum. Cell Mol Life Sci 81(1):90
Roy KR; Smith JD; Li S; Vonesch SC; Nguyen M; Burnett WT; Orsley KM; Lee CS; Haber JE; St Onge RP; Steinmetz LM, 2024. Dissecting quantitative trait nucleotides by saturation genome editing. bioRxiv.
Hale JJ; Matsui T; Goldstein I; Mullis MN; Roy KR; Ville CN; Miller D; Wang C; Reynolds T; Steinmetz LM; Levy SF; Ehrenreich IM, 2024. Genome-scale analysis of interactions between genetic perturbations and natural variation. bioRxiv.
Zhang ET; Wells KL; Bergman AJ; Ryan EE; Steinmetz LM; Baker JC, 2024. Uterine injury during diestrus leads to placental and embryonic defects in future pregnancies in mice†. Biol Reprod 110(4):819-833
McCulloch LH; Sambasivam V; Hughes AL; Annaluru N; Ramalingam S; Fanfani V; Lobzaev E; Mitchell LA; Cai J; Jiang H; LaCava J; Taylor MS; Bishai WR; Stracquadanio G; Steinmetz LM; Bader JS; Zhang W; Boeke JD; Chandrasegaran S, 2023. Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast synIX strains. Cell Genom 3(11):100419
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; Lieberman Aiden E; Greenleaf WJ; Leslie CS; Steinmetz LM; Kundaje A; Engreitz JM, 2023. An encyclopedia of enhancer-gene regulatory interactions in the human genome. bioRxiv.
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, 2023. Design, construction, and functional characterization of a tRNA neochromosome in yeast. Cell 186(24):5237-5253.e22
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, 2023. Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions. Cell 186(24):5220-5236.e16
Liu Z; Zhu C; Steinmetz LM; Wei W, 2023. Identification and quantification of small exon-containing isoforms in long-read RNA sequencing data. Nucleic Acids Res 51(20):e104
Pandey A; Galeone A; Han SY; Story BA; Consonni G; Mueller WF; Steinmetz LM; Vaccari T; Jafar-Nejad H, 2023. Gut barrier defects, intestinal immune hyperactivation and enhanced lipid catabolism drive lethality in NGLY1-deficient Drosophila. Nat Commun 14(1):5667
Tayyab M; Barrett D; van Riel G; Liu S; Reinius B; Scharfe C; Griffin P; Steinmetz LM; Javanmard M; Pelechano V, 2023. Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs. Sci Adv 9(36):eadi4997
Schraivogel D; Steinmetz LM; Parts L, 2023. Pooled Genome-Scale CRISPR Screens in Single Cells. Annu Rev Genet 57:223-244
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, 2023. Large scale microfluidic CRISPR screening for increased amylase secretion in yeast. Lab Chip 23(16):3704-3715
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, 2023. Mislocalization of pathogenic RBM20 variants in dilated cardiomyopathy is caused by loss-of-interaction with Transportin-3. Nat Commun 14(1):4312
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, 2023. Striated muscle-specific base editing enables correction of mutations causing dilated cardiomyopathy. Nat Commun 14(1):3714
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, 2023. Atlas of mRNA translation and decay for bacteria. Nat Microbiol 8(6):1123-1136
Pandey A; Galeone A; Han SY; Story BA; Consonni G; Mueller WF; Steinmetz LM; Vaccari T; Jafar-Nejad H, 2023. Gut barrier defects, increased intestinal innate immune response, and enhanced lipid catabolism drive lethality in N -glycanase 1 deficient Drosophila. bioRxiv.
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, 2023. A scalable, GMP-compatible, autologous organotypic cell therapy for Dystrophic Epidermolysis Bullosa. bioRxiv.
Li B; Zeis P; Zhang Y; Alekseenko A; Fürst E; Sanchez YP; Lin G; Tekkedil MM; Piazza I; Steinmetz LM; Pelechano V, 2023. Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation. Nat Commun 14(1):910
Schraivogel D; Steinmetz LM, 2023. Cell sorters see things more clearly now. Mol Syst Biol 19(3):e11254
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, 2022. Deep phenotyping of two preclinical mouse models and a cohort of RBM20 mutation carriers reveals no sex-dependent disease severity in RBM20 cardiomyopathy. Am J Physiol Heart Circ Physiol 323(6):H1296-H1310
Sedaghat-Hamedani F; Rebs S; Kayvanpour E; Zhu C; Amr A; Müller M; Haas J; Wu J; Steinmetz LM; Ehlermann P; Streckfuss-Bömeke K; Frey N; Meder B, 2022. Genotype Complements the Phenotype: Identification of the Pathogenicity of an LMNA Splice Variant by Nanopore Long-Read Sequencing in a Large DCM Family. Int J Mol Sci 23.
Müller M; Eghbalian R; Boeckel JN; Frese KS; Haas J; Kayvanpour E; Sedaghat-Hamedani F; Lackner MK; Tugrul OF; Ruppert T; Tappu R; Martins Bordalo D; Kneuer JM; Piekarek A; Herch S; Schudy S; Keller A; Grammes N; Bischof C; Klinke A; Cardoso-Moreira M; Kaessmann H; Katus HA; Frey N; Steinmetz LM; Meder B, 2022. NIMA-related kinase 9 regulates the phosphorylation of the essential myosin light chain in the heart. Nat Commun 13(1):6209
Carter JA; Strömich L; Peacey M; Chapin SR; Velten L; Steinmetz LM; Brors B; Pinto S; Meyer HV, 2022. Transcriptomic diversity in human medullary thymic epithelial cells. Nat Commun 13(1):4296
Steinmetz LM; Coselli JS, 2023. Endovascular Repair in Patients with Marfan Syndrome: Concerns Amid Controversy. Ann Vasc Surg 94:1-7
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, 2022. KIR(+)CD8(+) T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19. Science 376(6590):eabi9591
Brooks AN; Hughes AL; Clauder-Münster S; Mitchell LA; Boeke JD; Steinmetz LM, 2022. Transcriptional neighborhoods regulate transcript isoform lengths and expression levels. Science 375(6584):1000-1005
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, 2022. Assembly-dependent translation of subunits 6 (Atp6) and 9 (Atp9) of ATP synthase in yeast mitochondria. Genetics 220.
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, 2022. High-speed fluorescence image-enabled cell sorting. Science 375(6578):315-320
Li J; Zaslavsky M; Su Y; Sikora MJ; van Unen V; Christophersen A; Chiou SH; Chen L; Li J; Ji X; Wilhelmy J; McSween AM; Palanski BA; Aditya Mallajosyula VV; Dhondalay GKR; Bhamidipati K; Pai J; Kipp LB; Dunn JE; Hauser SL; Oksenberg JR; Satpathy AT; Robinson WH; Steinmetz LM; Khosla C; Utz PJ; Sollid LM; Heath JR; Fernandez-Becker NQ; Nadeau KC; Saligrama N; Davis MM, 2021. Human KIR (+) CD8 (+) T cells target pathogenic T cells in Celiac disease and are active in autoimmune diseases and COVID-19. bioRxiv.
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, 2022. Patient-derived gene and protein expression signatures of NGLY1 deficiency. J Biochem 171(2):187-199
Nandanan KG; Salim S; Pankajam AV; Shinohara M; Lin G; Chakraborty P; Farnaz A; Steinmetz LM; Shinohara A; Nishant KT, 2021. Regulation of Msh4-Msh5 association with meiotic chromosomes in budding yeast. Genetics 219.
Bieler J; Pozzorini C; Garcia J; Tuck AC; Macheret M; Willig A; Couraud S; Xing X; Menu P; Steinmetz LM; Payen L; Xu Z, 2021. High-Throughput Nucleotide Resolution Predictions of Assay Limitations Increase the Reliability and Concordance of Clinical Tests. JCO Clin Cancer Inform 5:1085-1095
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, 2022. High-throughput functional characterization of protein phosphorylation sites in yeast. Nat Biotechnol 40(3):382-390
King HW; Wells KL; Shipony Z; Kathiria AS; Wagar LE; Lareau C; Orban N; Capasso R; Davis MM; Steinmetz LM; James LK; Greenleaf WJ, 2021. Integrated single-cell transcriptomics and epigenomics reveals strong germinal center-associated etiology of autoimmune risk loci. Sci Immunol 6(64):eabh3768
Koelemen J; Gotthardt M; Steinmetz LM; Meder B, 2021. RBM20-Related Cardiomyopathy: Current Understanding and Future Options. J Clin Med 10.
Rosser JI; Tayyar R; Giardina R; Kolonoski P; Kenski D; Shen P; Steinmetz LM; Hung LY; Xiao W; Bains K; Morrison T; Madison A; Chang SI; Tompkins L; Pinsky BA; Holubar M, 2021. Case-control study evaluating risk factors for SARS-CoV-2 outbreak amongst healthcare personnel at a tertiary care center. Am J Infect Control 49(12):1457-1463
Zhu C; Wu J; Sun H; Briganti F; Meder B; Wei W; Steinmetz LM, 2021. Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms in cardiomyocytes. Nat Commun 12(1):4203
Horn SR; Passias PG; Passfall L; Lafage R; Smith JS; Poorman GW; Steinmetz LM; Bortz CA; Segreto FA; Diebo B; Hart R; Burton D; Shaffrey CI; Sciubba DM; Klineberg EO; Protopsaltis TS; Schwab FJ; Bess S; Lafage V; Ames C, 2021. Improvement in some Ames-ISSG cervical deformity classification modifier grades may correlate with clinical improvement. J Clin Neurosci 89:297-304
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, 2021. Author Correction: Dysregulated ribonucleoprotein granules promote cardiomyopathy in RBM20 gene-edited pigs. Nat Med 27(7):1309
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, 2021. Single-cell analyses reveal SARS-CoV-2 interference with intrinsic immune response in the human gut. Mol Syst Biol 17(4):e10232
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, 2021. The chaperone-binding activity of the mitochondrial surface receptor Tom70 protects the cytosol against mitoprotein-induced stress. Cell Rep 35(1):108936
Kubik S; Marques AC; Xing X; Silvery J; Bertelli C; De Maio F; Pournaras S; Burr T; Duffourd Y; Siemens H; Alloui C; Song L; Wenger Y; Saitta A; Macheret M; Smith EW; Menu P; Brayer M; Steinmetz LM; Si-Mohammed A; Chuisseu J; Stevens R; Constantoulakis P; Sali M; Greub G; Tiemann C; Pelechano V; Willig A; Xu Z, 2021. Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples. Clin Microbiol Infect 27(7):1036.e1-1036.e8
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, 2021. Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics. Nat Commun 12(1):1366
Gutmann F; Jann C; Pereira F; Johansson A; Steinmetz LM; Patil KR, 2021. CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate. Biotechnol Biofuels 14(1):41
Vonesch SC; Li S; Szu Tu C; Hennig BP; Dobrev N; Steinmetz LM, 2021. Fast and inexpensive whole-genome sequencing library preparation from intact yeast cells. G3 (Bethesda) 11.
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, 2021. A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae. Nucleic Acids Res 49(1):206-220
Wells KL; Miller CN; Gschwind AR; Wei W; Phipps JD; Anderson MS; Steinmetz LM, 2020. Combined transient ablation and single-cell RNA-sequencing reveals the development of medullary thymic epithelial cells. Elife 9.
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, 2020. Dysregulated ribonucleoprotein granules promote cardiomyopathy in RBM20 gene-edited pigs. Nat Med 26(11):1788-1800
Garrido-Godino AI; Gupta I; Gutiérrez-Santiago F; Martínez-Padilla AB; Alekseenko A; Steinmetz LM; Pérez-Ortín JE; Pelechano V; Navarro F, 2021. Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast. RNA Biol 18(8):1206-1220
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, 2020. iPSC Modeling of RBM20-Deficient DCM Identifies Upregulation of RBM20 as a Therapeutic Strategy. Cell Rep 32(10):108117
Wang J; Li B; Marques S; Steinmetz LM; Wei W; Pelechano V, 2020. TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes. Nucleic Acids Res 48(18):e104
Zuo E; Sun Y; Wei W; Yuan T; Ying W; Sun H; Yuan L; Steinmetz LM; Li Y; Yang H, 2020. GOTI, a method to identify genome-wide off-target effects of genome editing in mouse embryos. Nat Protoc 15(9):3009-3029
Schraivogel D; Gschwind AR; Milbank JH; Leonce DR; Jakob P; Mathur L; Korbel JO; Merten CA; Velten L; Steinmetz LM, 2020. Targeted Perturb-seq enables genome-scale genetic screens in single cells. Nat Methods 17(6):629-635
Calamak S; Ermis M; Sun H; Islam S; Sikora M; Nguyen M; Hasirci V; Steinmetz LM; Demirci U, 2020. A Circulating Bioreactor Reprograms Cancer Cells Toward a More Mesenchymal Niche. Adv Biosyst 4(2):e1900139
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, 2020. Loss of N-Glycanase 1 Alters Transcriptional and Translational Regulation in K562 Cell Lines. G3 (Bethesda) 10(5):1585-1597
Baccin C; Al-Sabah J; Velten L; Helbling PM; Grünschläger F; Hernández-Malmierca P; Nombela-Arrieta C; Steinmetz LM; Trumpp A; Haas S, 2020. Combined single-cell and spatial transcriptomics reveal the molecular, cellular and spatial bone marrow niche organization. Nat Cell Biol 22(1):38-48
Wei W; Hennig BP; Wang J; Zhang Y; Piazza I; Pareja Sanchez Y; Chabbert CD; Adjalley SH; Steinmetz LM; Pelechano V, 2019. Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast. Genome Res 29(12):1974-1984
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, 2020. Liver-specific deletion of Ngly1 causes abnormal nuclear morphology and lipid metabolism under food stress. Biochim Biophys Acta Mol Basis Dis 1866(3):165588
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; Steinmetz LM; Drewes G; Huber W, 2019. Biological plasticity rescues target activity in CRISPR knock outs. Nat Methods 16(11):1087-1093
Nadal-Ribelles M; Islam S; Wei W; Latorre P; Nguyen M; de Nadal E; Posas F; Steinmetz LM, 2019. Yeast Single-cell RNA-seq, Cell by Cell and Step by Step. Bio Protoc 9(17):e3359
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, 2019. Opposing T cell responses in experimental autoimmune encephalomyelitis. Nature 572(7770):481-487
Huang H; Sikora MJ; Islam S; Chowdhury RR; Chien YH; Scriba TJ; Davis MM; Steinmetz LM, 2019. Select sequencing of clonally expanded CD8(+) T cells reveals limits to clonal expansion. Proc Natl Acad Sci U S A 116(18):8995-9001
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; Schraivogel D; Schultz D; Wernick DG; Agashe D; Levi D; Zabezhinsky D; Russ D; Sass E; Tamar E; Herz E; Levy ED; Church GM; Yelin I; Nachman I; Gerst JE; Georgeson JM; Adamala KP; Steinmetz LM; Rübsam M; Ralser M; Klutstein M; Desai MM; Walunjkar N; Yin N; Aharon Hefetz N; Jakimo N; Snitser O; Adini O; Kumar P; Soo Hoo Smith R; Zeidan R; Hazan R; Rak R; Kishony R; Johnson S; Nouriel S; Vonesch SC; Foster S; Dagan T; Wein T; Karydis T; Wannier TM; Stiles T; Olin-Sandoval V; Mueller WF; Bar-On YM; Dahan O; Pilpel Y, 2019. Evolthon: A community endeavor to evolve lab evolution. PLoS Biol 17(3):e3000182
Parikh VN; Caleshu C; Reuter C; Lazzeroni LC; Ingles J; Garcia J; McCaleb K; Adesiyun T; Sedaghat-Hamedani F; Kumar S; Graw S; Gigli M; Stolfo D; Dal Ferro M; Ing AY; Nussbaum R; Funke B; Wheeler MT; Hershberger RE; Cook S; Steinmetz LM; Lakdawala NK; Taylor MRG; Mestroni L; Merlo M; Sinagra G; Semsarian C; Meder B; Judge DP; Ashley E, 2019. Regional Variation in RBM20 Causes a Highly Penetrant Arrhythmogenic Cardiomyopathy. Circ Heart Fail 12(3):e005371
Zuo E; Sun Y; Wei W; Yuan T; Ying W; Sun H; Yuan L; Steinmetz LM; Li Y; Yang H, 2019. Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science 364(6437):289-292
Nadal-Ribelles M; Islam S; Wei W; Latorre P; Nguyen M; de Nadal E; Posas F; Steinmetz LM, 2019. Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations. Nat Microbiol 4(4):683-692
Meza Gutierrez F; Simsek D; Mizrak A; Deutschbauer A; Braberg H; Johnson J; Xu J; Shales M; Nguyen M; Tamse-Kuehn R; Palm C; Steinmetz LM; Krogan NJ; Toczyski DP, 2018. Genetic analysis reveals functions of atypical polyubiquitin chains. Elife 7.
Kuprys TK; Steinmetz LM; Fischer CR; Protopsaltis TS; Passias PG; Goldstein JA; Bendo JA; Errico TJ; Buckland AJ, 2019. Preoperative Assessment of Bone Quality in Spine Deformity Surgery: Correlation With Clinical Practice and Published Recommendations. Spine (Phila Pa 1976) 44(12):E735-E741
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, 2018. High-frequency actionable pathogenic exome variants in an average-risk cohort. Cold Spring Harb Mol Case Stud 4.
Pękowska A; Klaus B; Xiang W; Severino J; Daigle N; Klein FA; Oleś M; Casellas R; Ellenberg J; Steinmetz LM; Bertone P; Huber W, 2018. Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency. Cell Syst 7(5):482-495.e10
Becker-Kettern J; Paczia N; Conrotte JF; Zhu C; Fiehn O; Jung PP; Steinmetz LM; Linster CL, 2018. NAD(P)HX repair deficiency causes central metabolic perturbations in yeast and human cells. FEBS J 285(18):3376-3401
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; Diedisheim M; Kyewski B; Steinmetz LM; Buus S; You S; Dubois-Laforgue D; Larger E; Beressi JP; Bruno G; Dotta F; Scharfmann R; Eizirik DL; Verdier Y; Vinh J; Mallone R, 2018. Conventional and Neo-antigenic Peptides Presented by β Cells Are Targeted by Circulating Naïve CD8+ T Cells in Type 1 Diabetic and Healthy Donors. Cell Metab 28(6):946-960.e6
Miller CN; Proekt I; von Moltke J; Wells KL; Rajpurkar AR; Wang H; Rattay K; Khan IS; Metzger TC; Pollack JL; Fries AC; Lwin WW; Wigton EJ; Parent AV; Kyewski B; Erle DJ; Hogquist KA; Steinmetz LM; Locksley RM; Anderson MS, 2018. Thymic tuft cells promote an IL-4-enriched medulla and shape thymocyte development. Nature 559(7715):627-631
Passias PG; Poorman GW; Vasquez-Montes D; Wang C; Jalai C; Horn SR; Steinmetz LM; Bortz CA; Segreto FA; Moon J; Zhou PL; Diebo BG; Vira S, 2018. Cluster analysis describes constellations of cardiac anomalies presenting in spinal anomaly patients. Acta Neurochir (Wien) 160(8):1613-1619
Horn SR; Liu TC; Horowitz JA; Oh C; Bortz CA; Segreto FA; Vasquez-Montes D; Steinmetz LM; Deflorimonte C; Vira S; Diebo BG; Neuman BJ; Raad M; Sciubba DM; Lafage R; Lafage V; Hassanzadeh H; Passias PG, 2018. Clinical Impact and Economic Burden of Hospital-Acquired Conditions Following Common Surgical Procedures. Spine (Phila Pa 1976) 43(22):E1358-E1363
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, 2018. Multiplexed precision genome editing with trackable genomic barcodes in yeast. Nat Biotechnol 36(6):512-520
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, 2018. HEx: A heterologous expression platform for the discovery of fungal natural products. Sci Adv 4(4):eaar5459
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, 2017. Inhibition of NGLY1 Inactivates the Transcription Factor Nrf1 and Potentiates Proteasome Inhibitor Cytotoxicity. ACS Cent Sci 3(11):1143-1155
Kim JH; Lee BB; Oh YM; Zhu C; Steinmetz LM; Lee Y; Kim WK; Lee SB; Buratowski S; Kim T, 2017. Erratum: Modulation of mRNA and lncRNA expression dynamics by the Set2-Rpd3S pathway. Nat Commun 8:16122
Hennig BP; Velten L; Racke I; Tu CS; Thoms M; Rybin V; Besir H; Remans K; Steinmetz LM, 2018. Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol. G3 (Bethesda) 8(1):79-89
Chabbert CD; Adjalley SH; Steinmetz LM; Pelechano V, 2018. Multiplexed ChIP-Seq Using Direct Nucleosome Barcoding: A Tool for High-Throughput Chromatin Analysis. Methods Mol Biol 1689:177-194
Dutta A; Lin G; Pankajam AV; Chakraborty P; Bhat N; Steinmetz LM; Nishant KT, 2017. Genome Dynamics of Hybrid Saccharomyces cerevisiae During Vegetative and Meiotic Divisions. G3 (Bethesda) 7(11):3669-3679
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, 2017. Assembly of functionally integrated human forebrain spheroids. Nature 545(7652):54-59
Tay TL; Mai D; Dautzenberg J; Fernández-Klett F; Lin G; Sagar; 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, 2017. A new fate mapping system reveals context-dependent random or clonal expansion of microglia. Nat Neurosci 20(6):793-803
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, 2017. Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates. Nature 544(7649):245-249
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, 2017. Human haematopoietic stem cell lineage commitment is a continuous process. Nat Cell Biol 19(4):271-281
Chakraborty P; Pankajam AV; Lin G; Dutta A; Krishnaprasad GN; Tekkedil MM; Shinohara A; Steinmetz LM; Nishant KT, 2017. Modulating Crossover Frequency and Interference for Obligate Crossovers in Saccharomyces cerevisiae Meiosis. G3 (Bethesda) 7(5):1511-1524
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, 2017. A method for high-throughput production of sequence-verified DNA libraries and strain collections. Mol Syst Biol 13(2):913
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, 2017. The State of Systems Genetics in 2017. Cell Syst 4(1):7-15
Klopf E; Schmidt HA; Clauder-Münster S; Steinmetz LM; Schüller C, 2017. INO80 represses osmostress induced gene expression by resetting promoter proximal nucleosomes. Nucleic Acids Res 45(7):3752-3766
Kim JH; Lee BB; Oh YM; Zhu C; Steinmetz LM; Lee Y; Kim WK; Lee SB; Buratowski S; Kim T, 2016. Modulation of mRNA and lncRNA expression dynamics by the Set2-Rpd3S pathway. Nat Commun 7:13534
Huang Z; Ayday E; Lin H; Aiyar RS; Molyneaux A; Xu Z; Fellay J; Steinmetz LM; Hubaux JP, 2016. A privacy-preserving solution for compressed storage and selective retrieval of genomic data. Genome Res 26(12):1687-1696
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, 2016. A global genetic interaction network maps a wiring diagram of cellular function. Science 353.
Brooks AN; Mueller WF; Steinmetz LM, 2016. SYGNALing a Red Light for Glioblastoma. Cell Syst 3(2):118-120
Chen Y; Pai AA; Herudek J; Lubas M; Meola N; Järvelin AI; Andersson R; Pelechano V; Steinmetz LM; Jensen TH; Sandelin A, 2016. Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters. Nat Genet 48(9):984-94
Gupta S; Radhakrishnan A; Nitin R; Raharja-Liu P; Lin G; Steinmetz LM; Gagneur J; Sinha H, 2016. Meiotic Interactors of a Mitotic Gene TAO3 Revealed by Functional Analysis of its Rare Variant. G3 (Bethesda) 6(8):2255-63
Huber F; Bunina D; Gupta I; Khmelinskii A; Meurer M; Theer P; Steinmetz LM; Knop M, 2016. Protein Abundance Control by Non-coding Antisense Transcription. Cell Rep 15(12):2625-36
Gupta I; Villanyi Z; Kassem S; Hughes C; Panasenko OO; Steinmetz LM; Collart MA, 2016. Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex. Cell Rep 15(8):1782-94
Chlamydas S; Holz H; Samata M; Chelmicki T; Georgiev P; Pelechano V; Dündar F; Dasmeh P; Mittler G; Cadete FT; Ramírez F; Conrad T; Wei W; Raja S; Manke T; Luscombe NM; Steinmetz LM; Akhtar A, 2016. Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation. Nat Struct Mol Biol 23(6):580-9
Chabbert CD; Steinmetz LM; Klaus B, 2016. DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies. PeerJ 4:e1981
Steinmetz LM; Jones A, 2016. Sensing a revolution. Mol Syst Biol 12(4):867
Smith JD; Suresh S; Schlecht U; Wu M; Wagih O; Peltz G; Davis RW; Steinmetz LM; Parts L; St Onge RP, 2016. Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design. Genome Biol 17:45
Adjalley SH; Chabbert CD; Klaus B; Pelechano V; Steinmetz LM, 2016. Landscape and Dynamics of Transcription Initiation in the Malaria Parasite Plasmodium falciparum. Cell Rep 14(10):2463-75
Pelechano V; Wei W; Steinmetz LM, 2016. Genome-wide quantification of 5'-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics. Nat Protoc 11(2):359-76
Holmes RK; Tuck AC; Zhu C; Dunn-Davies HR; Kudla G; Clauder-Munster S; Granneman S; Steinmetz LM; Guthrie C; Tollervey D, 2015. Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough. PLoS Genet 11(12):e1005735
Rege M; Subramanian V; Zhu C; Hsieh TH; Weiner A; Friedman N; Clauder-Münster S; Steinmetz LM; Rando OJ; Boyer LA; Peterson CL, 2015. Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis. Cell Rep 13(8):1610-22
Baday M; Calamak S; Durmus NG; Davis RW; Steinmetz LM; Demirci U, 2016. Integrating Cell Phone Imaging with Magnetic Levitation (i-LEV) for Label-Free Blood Analysis at the Point-of-Living. Small 12(9):1222-1229
Wilkening S; Pelechano V; Steinmetz LM, 2016. Genome-Wide Identification of Alternative Polyadenylation Events Using 3'T-Fill. Methods Mol Biol 1358:295-302
Castello A; Horos R; Strein C; Fischer B; Eichelbaum K; Steinmetz LM; Krijgsveld J; Hentze MW, 2016. Comprehensive Identification of RNA-Binding Proteins by RNA Interactome Capture. Methods Mol Biol 1358:131-9
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. Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Cell 162(5):1051-65
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, 2015. Inflammation-Induced Emergency Megakaryopoiesis Driven by Hematopoietic Stem Cell-like Megakaryocyte Progenitors. Cell Stem Cell 17(4):422-34
Brennecke P; Reyes A; Pinto S; Rattay K; Nguyen M; Küchler R; Huber W; Kyewski B; Steinmetz LM, 2015. Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells. Nat Immunol 16(9):933-41
Inci F; Filippini C; Baday M; Ozen MO; Calamak S; Durmus NG; Wang S; Hanhauser E; Hobbs KS; Juillard F; Kuang PP; Vetter ML; Carocci M; Yamamoto HS; Takagi Y; Yildiz UH; Akin D; Wesemann DR; Singhal A; Yang PL; Nibert ML; Fichorova RN; Lau DT; Henrich TJ; Kaye KM; Schachter SC; Kuritzkes DR; Steinmetz LM; Gambhir SS; Davis RW; Demirci U, 2015. Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics. Proc Natl Acad Sci U S A 112(32):E4354-63
Durmus NG; Tekin HC; Guven S; Sridhar K; Arslan Yildiz A; Calibasi G; Ghiran I; Davis RW; Steinmetz LM; Demirci U, 2015. Magnetic levitation of single cells. Proc Natl Acad Sci U S A 112(28):E3661-8
Schmid M; Olszewski P; Pelechano V; Gupta I; Steinmetz LM; Jensen TH, 2015. The Nuclear PolyA-Binding Protein Nab2p Is Essential for mRNA Production. Cell Rep 12(1):128-139
Pelechano V; Wei W; Steinmetz LM, 2015. Widespread Co-translational RNA Decay Reveals Ribosome Dynamics. Cell 161(6):1400-12
Velten L; Anders S; Pekowska A; Järvelin AI; Huber W; Pelechano V; Steinmetz LM, 2015. Single-cell polyadenylation site mapping reveals 3' isoform choice variability. Mol Syst Biol 11(6):812
Gupta S; Radhakrishnan A; Raharja-Liu P; Lin G; Steinmetz LM; Gagneur J; Sinha H, 2015. Temporal expression profiling identifies pathways mediating effect of causal variant on phenotype. PLoS Genet 11(6):e1005195
Lasserre JP; Dautant A; Aiyar RS; Kucharczyk R; Glatigny A; Tribouillard-Tanvier D; Rytka J; Blondel M; Skoczen N; Reynier P; Pitayu L; Rötig A; Delahodde A; Steinmetz LM; Dujardin G; Procaccio V; di Rago JP, 2015. Yeast as a system for modeling mitochondrial disease mechanisms and discovering therapies. Dis Model Mech 8(6):509-26
Bader DM; Wilkening S; Lin G; Tekkedil MM; Dietrich K; Steinmetz LM; Gagneur J, 2015. Negative feedback buffers effects of regulatory variants. Mol Syst Biol 11(1):785
Chabbert CD; Adjalley SH; Klaus B; Fritsch ES; Gupta I; Pelechano V; Steinmetz LM, 2015. A high-throughput ChIP-Seq for large-scale chromatin studies. Mol Syst Biol 11(1):777
Jordán-Pla A; Gupta I; de Miguel-Jiménez L; Steinmetz LM; Chávez S; Pelechano V; Pérez-Ortín JE, 2015. Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle. Nucleic Acids Res 43(2):787-802
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, 2014. Mitochondrial protein sorting as a therapeutic target for ATP synthase disorders. Nat Commun 5:5585
Colin J; Candelli T; Porrua O; Boulay J; Zhu C; Lacroute F; Steinmetz LM; Libri D, 2014. Roadblock termination by reb1p restricts cryptic and readthrough transcription. Mol Cell 56(5):667-80
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, 2015. The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development. Nucleic Acids Res 43(1):115-28
Krishnaprasad GN; Anand MT; Lin G; Tekkedil MM; Steinmetz LM; Nishant KT, 2015. Variation in crossover frequencies perturb crossover assurance without affecting meiotic chromosome segregation in Saccharomyces cerevisiae. Genetics 199(2):399-412
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, 2014. Expression of nuclear and mitochondrial genes encoding ATP synthase is synchronized by disassembly of a multisynthetase complex. Mol Cell 56(6):763-76
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, 2014. Transcription mediated insulation and interference direct gene cluster expression switches. Elife 3:e03635
Hughes CS; Foehr S; Garfield DA; Furlong EE; Steinmetz LM; Krijgsveld J, 2014. Ultrasensitive proteome analysis using paramagnetic bead technology. Mol Syst Biol 10(10):757
Moore LS; Wei W; Stolovicki E; Benbenishty T; Wilkening S; Steinmetz LM; Braun E; David L, 2014. Induced mutations in yeast cell populations adapting to an unforeseen challenge. PLoS One 9(10):e111133
David L; Clauder-Münster S; Steinmetz LM, 2014. High-density tiling microarray analysis of the full transcriptional activity of yeast. Methods Mol Biol 1205:257-73
Fritsch ES; Chabbert CD; Klaus B; Steinmetz LM, 2014. A genome-wide map of mitochondrial DNA recombination in yeast. Genetics 198(2):755-71
Pelechano V; Wei W; Jakob P; Steinmetz LM, 2014. Genome-wide identification of transcript start and end sites by transcript isoform sequencing. Nat Protoc 9(7):1740-59
Parts L; Liu YC; Tekkedil MM; Steinmetz LM; Caudy AA; Fraser AG; Boone C; Andrews BJ; Rosebrock AP, 2014. Heritability and genetic basis of protein level variation in an outbred population. Genome Res 24(8):1363-70
Gupta I; Clauder-Münster S; Klaus B; Järvelin AI; Aiyar RS; Benes V; Wilkening S; Huber W; Pelechano V; Steinmetz LM, 2014. Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions. Mol Syst Biol 10(2):719
Nadal-Ribelles M; Solé C; Xu Z; Steinmetz LM; de Nadal E; Posas F, 2014. Control of Cdc28 CDK1 by a stress-induced lncRNA. Mol Cell 53(4):549-61
Castelnuovo M; Zaugg JB; Guffanti E; Maffioletti A; Camblong J; Xu Z; Clauder-Münster S; Steinmetz LM; Luscombe NM; Stutz F, 2014. Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast. Nucleic Acids Res 42(7):4348-62
Bhatia A; Yadav A; Zhu C; Gagneur J; Radhakrishnan A; Steinmetz LM; Bhanot G; Sinha H, 2014. Yeast growth plasticity is regulated by environment-specific multi-QTL interactions. G3 (Bethesda) 4(5):769-77
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, 2014. An evaluation of high-throughput approaches to QTL mapping in Saccharomyces cerevisiae. Genetics 196(3):853-65
Lenstra TL; Tudek A; Clauder S; Xu Z; Pachis ST; van Leenen D; Kemmeren P; Steinmetz LM; Libri D; Holstege FC, 2013. The role of Ctk1 kinase in termination of small non-coding RNAs. PLoS One 8(12):e80495
Pelechano V; Steinmetz LM, 2013. Gene regulation by antisense transcription. Nat Rev Genet 14(12):880-93
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, 2013. Extensive variation in chromatin states across humans. Science 342(6159):750-2
Fehrmann S; Bottin-Duplus H; Leonidou A; Mollereau E; Barthelaix A; Wei W; Steinmetz LM; Yvert G, 2013. Natural sequence variants of yeast environmental sensors confer cell-to-cell expression variability. Mol Syst Biol 9:695
Gagneur J; Stegle O; Zhu C; Jakob P; Tekkedil MM; Aiyar RS; Schuon AK; Pe'er D; Steinmetz LM, 2013. Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype. PLoS Genet 9(9):e1003803
Reyes A; Anders S; Weatheritt RJ; Gibson TJ; Steinmetz LM; Huber W, 2013. Drift and conservation of differential exon usage across tissues in primate species. Proc Natl Acad Sci U S A 110(38):15377-82
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, 2013. Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality. Nat Struct Mol Biol 20(8):923-8
Pelechano V; Wei W; Steinmetz LM, 2013. Extensive transcriptional heterogeneity revealed by isoform profiling. Nature 497(7447):127-31
David L; Ben-Harosh Y; Stolovicki E; Moore LS; Nguyen M; Tamse R; Dean J; Mancera E; Steinmetz LM; Braun E, 2013. Multiple genomic changes associated with reorganization of gene regulation and adaptation in yeast. Mol Biol Evol 30(7):1514-26
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, 2013. The genomic and transcriptomic landscape of a HeLa cell line. G3 (Bethesda) 3(8):1213-24
Castello A; Horos R; Strein C; Fischer B; Eichelbaum K; Steinmetz LM; Krijgsveld J; Hentze MW, 2013. System-wide identification of RNA-binding proteins by interactome capture. Nat Protoc 8(3):491-500
Wilkening S; Tekkedil MM; Lin G; Fritsch ES; Wei W; Gagneur J; Lazinski DW; Camilli A; Steinmetz LM, 2013. Genotyping 1000 yeast strains by next-generation sequencing. BMC Genomics 14:90
Wilkening S; Pelechano V; Järvelin AI; Tekkedil MM; Anders S; Benes V; Steinmetz LM, 2013. An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Res 41(5):e65
Hobson DJ; Wei W; Steinmetz LM; Svejstrup JQ, 2012. RNA polymerase II collision interrupts convergent transcription. Mol Cell 48(3):365-74
Abraham AL; Nagarajan M; Veyrieras JB; Bottin H; Steinmetz LM; Yvert G, 2012. Genetic modifiers of chromatin acetylation antagonize the reprogramming of epi-polymorphisms. PLoS Genet 8(9):e1002958
Tan-Wong SM; Zaugg JB; Camblong J; Xu Z; Zhang DW; Mischo HE; Ansari AZ; Luscombe NM; Steinmetz LM; Proudfoot NJ, 2012. Gene loops enhance transcriptional directionality. Science 338(6107):671-5
Gudipati RK; Xu Z; Lebreton A; Séraphin B; Steinmetz LM; Jacquier A; Libri D, 2012. Extensive degradation of RNA precursors by the exosome in wild-type cells. Mol Cell 48(3):409-21
Lamacchia M; Clayton JR; Wang-Sattler R; Steinmetz LM; Levashina EA; Blandin SA, 2013. Silencing of genes and alleles by RNAi in Anopheles gambiae. Methods Mol Biol 923:161-76
Kim T; Xu Z; Clauder-Münster S; Steinmetz LM; Buratowski S, 2012. Set3 HDAC mediates effects of overlapping noncoding transcription on gene induction kinetics. Cell 150(6):1158-69
Pelechano V; Wilkening S; Järvelin AI; Tekkedil MM; Steinmetz LM, 2012. Genome-wide polyadenylation site mapping. Methods Enzymol 513:271-96
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, 2012. Experimental relocation of the mitochondrial ATP9 gene to the nucleus reveals forces underlying mitochondrial genome evolution. PLoS Genet 8(8):e1002876
Delhomme N; Padioleau I; Furlong EE; Steinmetz LM, 2012. easyRNASeq: a bioconductor package for processing RNA-Seq data. Bioinformatics 28(19):2532-3
Schmid M; Poulsen MB; Olszewski P; Pelechano V; Saguez C; Gupta I; Steinmetz LM; Moore C; Jensen TH, 2012. Rrp6p controls mRNA poly(A) tail length and its decoration with poly(A) binding proteins. Mol Cell 47(2):267-80
Castello A; Fischer B; Eichelbaum K; Horos R; Beckmann BM; Strein C; Davey NE; Humphreys DT; Preiss T; Steinmetz LM; Krijgsveld J; Hentze MW, 2012. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 149(6):1393-406
Heise F; Chung HR; Weber JM; Xu Z; Klein-Hitpass L; Steinmetz LM; Vingron M; Ehrenhofer-Murray AE, 2012. Genome-wide H4 K16 acetylation by SAS-I is deposited independently of transcription and histone exchange. Nucleic Acids Res 40(1):65-74
David L; Clauder-Münster S; Steinmetz LM, 2011. Genome-wide transcriptome analysis in yeast using high-density tiling arrays. Methods Mol Biol 759:107-23
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, 2011. A yeast-based assay identifies drugs active against human mitochondrial disorders. Proc Natl Acad Sci U S A 108(29):11989-94
Marvin MC; Clauder-Münster S; Walker SC; Sarkeshik A; Yates JR 3rd; Steinmetz LM; Engelke DR, 2011. Accumulation of noncoding RNA due to an RNase P defect in Saccharomyces cerevisiae. RNA 17(8):1441-50
Wei W; Pelechano V; Järvelin AI; Steinmetz LM, 2011. Functional consequences of bidirectional promoters. Trends Genet 27(7):267-76
Mancera E; Bourgon R; Huber W; Steinmetz LM, 2011. Genome-wide survey of post-meiotic segregation during yeast recombination. Genome Biol 12(4):R36
Xu Z; Wei W; Gagneur J; Clauder-Münster S; Smolik M; Huber W; Steinmetz LM, 2011. Antisense expression increases gene expression variability and locus interdependency. Mol Syst Biol 7:468
Lardenois A; Liu Y; Walther T; Chalmel F; Evrard B; Granovskaia M; Chu A; Davis RW; Steinmetz LM; Primig M, 2011. Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6. Proc Natl Acad Sci U S A 108(3):1058-63
Nishant KT; Wei W; Mancera E; Argueso JL; Schlattl A; Delhomme N; Ma X; Bustamante CD; Korbel JO; Gu Z; Steinmetz LM; Alani E, 2010. The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis. PLoS Genet 6(9):e1001109
Nagarajan M; Veyrieras JB; de Dieuleveult M; Bottin H; Fehrmann S; Abraham AL; Croze S; Steinmetz LM; Gidrol X; Yvert G, 2010. Natural single-nucleosome epi-polymorphisms in yeast. PLoS Genet 6(4):e1000913
Zheng W; Zhao H; Mancera E; Steinmetz LM; Snyder M, 2010. Genetic analysis of variation in transcription factor binding in yeast. Nature 464(7292):1187-91
Granovskaia MV; Jensen LJ; Ritchie ME; Toedling J; Ning Y; Bork P; Huber W; Steinmetz LM, 2010. High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Genome Biol 11(3):R24
Blandin SA; Wang-Sattler R; Lamacchia M; Gagneur J; Lycett G; Ning Y; Levashina EA; Steinmetz LM, 2009. Dissecting the genetic basis of resistance to malaria parasites in Anopheles gambiae. Science 326(5949):147-50
Camblong J; Beyrouthy N; Guffanti E; Schlaepfer G; Steinmetz LM; Stutz F, 2009. Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Genes Dev 23(13):1534-45
Gagneur J; Sinha H; Perocchi F; Bourgon R; Huber W; Steinmetz LM, 2009. Genome-wide allele- and strand-specific expression profiling. Mol Syst Biol 5:274
Bourgon R; Mancera E; Brozzi A; Steinmetz LM; Huber W, 2009. Array-based genotyping in S.cerevisiae using semi-supervised clustering. Bioinformatics 25(8):1056-62
Neil H; Malabat C; d'Aubenton-Carafa Y; Xu Z; Steinmetz LM; Jacquier A, 2009. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457(7232):1038-42
Xu Z; Wei W; Gagneur J; Perocchi F; Clauder-Münster S; Camblong J; Guffanti E; Stutz F; Huber W; Steinmetz LM, 2009. Bidirectional promoters generate pervasive transcription in yeast. Nature 457(7232):1033-7
Aiyar RS; Gagneur J; Steinmetz LM, 2008. Identification of mitochondrial disease genes through integrative analysis of multiple datasets. Methods 46(4):248-55
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, 2008. Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast. Genetics 180(3):1661-70
Mancera E; Bourgon R; Brozzi A; Huber W; Steinmetz LM, 2008. High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature 454(7203):479-85
Perocchi F; Mancera E; Steinmetz LM, 2008. Systematic screens for human disease genes, from yeast to human and back. Mol Biosyst 4(1):18-29
Wang-Sattler R; Blandin S; Ning Y; Blass C; Dolo G; Touré YT; delle Torre A; Lanzaro GC; Steinmetz LM; Kafatos FC; Zheng L, 2007. Mosaic genome architecture of the Anopheles gambiae species complex. PLoS One 2(11):e1249
Perocchi F; Xu Z; Clauder-Münster S; Steinmetz LM, 2007. Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res 35(19):e128
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, 2007. Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proc Natl Acad Sci U S A 104(31):12825-30
Perocchi F; Jensen LJ; Gagneur J; Ahting U; von Mering C; Bork P; Prokisch H; Steinmetz LM, 2006. Assessing systems properties of yeast mitochondria through an interaction map of the organelle. PLoS Genet 2(10):e170
Huber W; Toedling J; Steinmetz LM, 2006. Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics 22(16):1963-70
Gagneur J; David L; Steinmetz LM, 2006. Capturing cellular machines by systematic screens of protein complexes. Trends Microbiol 14(8):336-9
David L; Huber W; Granovskaia M; Toedling J; Palm CJ; Bofkin L; Jones T; Davis RW; Steinmetz LM, 2006. A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A 103(14):5320-5
Sinha H; Nicholson BP; Steinmetz LM; McCusker JH, 2006. Complex genetic interactions in a quantitative trait locus. PLoS Genet 2(2):e13
Jensen LJ; Steinmetz LM, 2005. Re-analysis of data and its integration. FEBS Lett 579(8):1802-7
Gu Z; David L; Petrov D; Jones T; Davis RW; Steinmetz LM, 2005. Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 102(4):1092-7
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, 2004. Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol 2(6):e160
Steinmetz LM; Davis RW, 2004. Maximizing the potential of functional genomics. Nat Rev Genet 5(3):190-201
Gu Z; Steinmetz LM; Gu X; Scharfe C; Davis RW; Li WH, 2003. Role of duplicate genes in genetic robustness against null mutations. Nature 421(6918):63-6
Steinmetz LM; Deutschbauer AM, 2002. Gene function on a genomic scale. J Chromatogr B Analyt Technol Biomed Life Sci 782(1-2):151-63
Steinmetz LM; Scharfe C; Deutschbauer AM; Mokranjac D; Herman ZS; Jones T; Chu AM; Giaever G; Prokisch H; Oefner PJ; Davis RW, 2002. Systematic screen for human disease genes in yeast. Nat Genet 31(4):400-4
Fraser HB; Hirsh AE; Steinmetz LM; Scharfe C; Feldman MW, 2002. Evolutionary rate in the protein interaction network. Science 296(5568):750-2
Steinmetz LM; Sinha H; Richards DR; Spiegelman JI; Oefner PJ; McCusker JH; Davis RW, 2002. Dissecting the architecture of a quantitative trait locus in yeast. Nature 416(6878):326-30
Steinmetz LM; Davis RW, 2000. High-density arrays and insights into genome function. Biotechnol Genet Eng Rev 17:109-46
Steinmetz LM; Mindrinos M; Oefner PJ, 2000. Combining genome sequences and new technologies for dissecting the genetics of complex phenotypes. Trends Plant Sci 5(9):397-401
