All Publications

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.

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 10:757

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 10:719

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