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. doi: 10.1038/s41592-020-0837-5
Europe PMC | doi

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) doi: 10.1534/g3.119.401031
Europe PMC | doi

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) doi: 10.1002/adbi.201900139
Europe PMC | doi

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. doi: 10.1038/s41556-019-0439-6
Europe PMC | doi

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. doi: 10.1101/gr.243378.118
Europe PMC | doi

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. (2019)

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

Biochim Biophys Acta Mol Basis Dis 1866(3) doi: 10.1016/j.bbadis.2019.165588
Europe PMC | doi

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. (2019)

Biological plasticity rescues target activity in CRISPR knock outs.

Nat. Methods 16(11) doi: 10.1038/s41592-019-0614-5
Europe PMC | doi

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-protocol 9(17) doi: 10.21769/BioProtoc.3359
doi

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. doi: 10.1038/s41586-019-1467-x
Europe PMC | doi

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. doi: 10.1073/pnas.1902649116
Europe PMC | doi

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. doi: 10.1038/s41564-018-0346-9
Europe PMC | doi

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. (2019)

Evolthon: a community endeavor to evolve lab evolution.

PLoS Biol. 17(3) doi: 10.1371/journal.pbio.3000182
Europe PMC | doi

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) doi: 10.1126/science.aav9973
Europe PMC | doi

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(6) doi: 10.1101/mcs.a003178
Europe PMC | doi

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. (2018)

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

Cell Metab 28(6):946-960.e6. doi: 10.1016/j.cmet.2018.07.007
Europe PMC | doi

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. doi: 10.1016/j.cels.2018.09.003
Europe PMC | doi

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) doi: 10.1111/febs.14631
Europe PMC | doi

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)

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

Elife e38517 doi: 10.7554/eLife.38517
Europe PMC | doi

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. (2018)

Rpd3L HDAC links H3K4me3 to transcriptional repression memory.

Nucleic Acids Res. 46(16):8261-8274. doi: 10.1093/nar/gky573
Europe PMC | doi

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) doi: 10.1038/nbt.4137
Europe PMC | doi

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) doi: 10.1126/sciadv.aar5459
Europe PMC | doi

Hennig BP, Velten L, Racke I, Szu Tu C, 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) doi: 10.1534/g3.117.300257
Europe PMC | doi

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

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. doi: 10.1021/acscentsci.7b00224
Europe PMC | doi

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) doi: 10.1534/g3.117.1135
Europe PMC | doi

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. (2017)

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

Nat. Neurosci. 20(6) doi: 10.1038/nn.4547
Europe PMC | doi

Chakraborty P, Pankajam AV, Lin G, Dutta A, Nandanan KG, Tekkedil MM, Shinohara A, Steinmetz LM, Thazath NK. (2017)

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

G3 (Bethesda) 7(5) doi: 10.1534/g3.117.040071
Europe PMC | doi

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. doi: 10.1038/nature22330
Europe PMC | doi

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. doi: 10.1093/nar/gkw1292
Europe PMC | doi

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. doi: 10.1038/nature21722
Europe PMC | doi

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):1-271. doi: 10.1038/ncb3493
Europe PMC | doi

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. doi: 10.15252/msb.20167233
Europe PMC | doi

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. doi: 10.1016/j.cels.2017.01.005
Europe PMC | doi

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 doi: 10.1038/ncomms13534
Europe PMC | doi

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(6306):1381-aaf1420-14. doi: 10.1126/science.aaf1420
Europe PMC | doi

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):984-994. doi: 10.1038/ng.3616
Europe PMC | doi

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):2625-2636. doi: 10.1016/j.celrep.2016.05.043
Europe PMC | doi

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) doi: 10.1534/g3.116.029900
Europe PMC | doi

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. (2016)

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

NAT STRUCT MOL BIOL 23(6):580-589. doi: 10.1038/nsmb.3233
Europe PMC | doi

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):1782-1794. doi: 10.1016/j.celrep.2016.04.055
Europe PMC | doi

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. (2016)

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

Nucleic Acids Res. 44(8):3643-3658. doi: 10.1093/nar/gkv1512
Europe PMC | doi

Chabbert CD, Steinmetz LM, Klaus B. (2016)

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

PeerJ 4:1-12. doi: 10.7717/peerj.1981
Europe PMC | doi

Lars M. Steinmetz & Allan Jones. (2016)

Sensing a revolution.

Mol Syst Biol. 12(4) doi: 10.15252/msb.20166873
Europe PMC | doi

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):2463-2475. doi: 10.1016/j.celrep.2016.02.025
Europe PMC | doi

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(1) doi: 10.1186/s13059-016-0900-9
Europe PMC | doi

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):359-376. doi: 10.1038/nprot.2016.026
Europe PMC | doi

Brooks AN, Mueller WF, Steinmetz LM. (2016)

SYGNALing a Red Light for Glioblastoma.

Cell Sys 3(2):118-120. doi: 10.1016/j.cels.2016.08.002
Europe PMC | doi

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. 1358:131-139. doi: 10.1007/978-1-4939-3067-8_8
Europe PMC | doi

Wilkening S, Pelechano V, Steinmetz LM. (2016)

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

Methods Mol. Biol. 1358:295-302. doi: 10.1007/978-1-4939-3067-8_18
Europe PMC | doi

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) doi: 10.1371/journal.pgen.1005735
Europe PMC | doi

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):1610-1622. doi: 10.1016/j.celrep.2015.10.030
Europe PMC | doi

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):422-434. doi: 10.1016/j.stem.2015.07.007
Europe PMC | doi

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):1051-1065. doi: 10.1016/j.cell.2015.07.048
Europe PMC | doi

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):933-941. doi: 10.1038/ni.3246
Europe PMC | doi

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. doi: 10.1016/j.celrep.2015.06.008
Europe PMC | doi

Pelechano V, Wei W, Steinmetz LM. (2015)

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics.

Cell 161(6):1400-1412. doi: 10.1016/j.cell.2015.05.008
Europe PMC | doi

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) doi: 10.15252/msb.20156198
Europe PMC | doi

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) doi: 10.1371/journal.pgen.1005195
Europe PMC | doi

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. (2015)

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

Dis. Model. Mech. 8(6):509-526. doi: 10.1242/dmm.020438
Europe PMC | doi

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) doi: 10.15252/msb.20145844
Europe PMC | doi

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):1-14. doi: 10.15252/msb.20145776
Europe PMC | doi

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) doi: 10.1093/nar/gku1349
Europe PMC | doi

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) doi: 10.1093/nar/gku1185
Europe PMC | doi

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. doi: 10.1038/ncomms6585
Europe PMC | doi

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):763-776. doi: 10.1016/j.molcel.2014.10.015
Europe PMC | doi

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):667-680. doi: 10.1016/j.molcel.2014.10.026
Europe PMC | doi

Krishnaprasad GN, Anand MT, Lin G, Tekkedil MM, Steinmetz LM, Nishant KT. (2014)

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

Genetics 199(2) doi: 10.1534/genetics.114.172320
Europe PMC | doi

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 doi: 10.7554/elife.03635
Europe PMC | doi

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) doi: 10.15252/msb.20145625
Europe PMC | doi

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) doi: 10.1371/journal.pone.0111133
Europe PMC | doi

Villanyi Z, Ribaud V, Kassem S, Panasenko OO, Pahi Z, Gupta I, Steinmetz L, Boros I, Collart MA. (2014)

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

PLoS Genet. 10(10):e1004569. doi: 10.1371/journal.pgen.1004569
Europe PMC | doi

Fritsch ES, Chabbert CD, Klaus B, Steinmetz LM. (2014)

A Genome-Wide Map of Mitochondrial DNA Recombination in Yeast

Genetics 198(2):755-771. doi: 10.1534/genetics.114.166637
Europe PMC | doi

Parts L, Liu YC, Tekkedil M, 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):1363-1370. doi: 10.1101/gr.170506.113
Europe PMC | doi

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):1740-1759. doi: 10.1038/nprot.2014.121
Europe PMC | doi

Bhatia A, Yadav A, Gagneur J, Zhu C, Steinmetz LM, Bhanot G, Sinha H. (2014)

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

G3 (Bethesda) 4(5):769-777. doi: 10.1534/g3.113.009142
Europe PMC | doi

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):4348-4362. doi: 10.1093/nar/gku100
Europe PMC | doi

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):853-865. doi: 10.1534/genetics.113.160291
Europe PMC | doi

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. doi: 10.1002/msb.135068
Europe PMC | doi

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):549-561. doi: 10.1016/j.molcel.2014.01.006
Europe PMC | doi

Pelechano V, Steinmetz LM. (2013)

Gene regulation by antisense transcription

Nat. Rev. Genet. 14(12):880-893. doi: 10.1038/nrg3594
Europe PMC | doi

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):750-752. doi: 10.1126/science.1242510
Europe PMC | doi

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):15377-15382. doi: 10.1073/pnas.1307202110
Europe PMC | doi

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):1213-1224. doi: 10.1534/g3.113.005777
Europe PMC | doi

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):923-928. doi: 10.1038/nsmb.2640
Europe PMC | doi

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):1514-1526. doi: 10.1093/molbev/mst071
Europe PMC | doi

Wilkening S, Pelechano V, Jarvelin AI, Tekkedil MM, Anders S, Benes V, Steinmetz LM. (2013)

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

Nucleic Acids Res 41(12):6370. doi: 10.1093/nar/gkt364
doi

Pelechano V, Wei W, Steinmetz LM. (2013)

Extensive transcriptional heterogeneity revealed by isoform profiling

Nature 497(7447):127-131. doi: 10.1038/nature12121
Europe PMC | doi

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. doi: 10.1038/nprot.2013.020
Europe PMC | doi

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(12):6370. doi: 10.1093/nar/gks1249
Europe PMC | doi

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. doi: 10.1038/msb.2013.53
Europe PMC | doi

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. doi: 10.1371/journal.pgen.1003803
Europe PMC | doi

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. 923:161-176. doi: 10.1007/978-1-62703-026-7_11
Europe PMC | doi

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. doi: 10.1371/journal.pone.0080495
Europe PMC | doi

Reyes A, Blume Carolin, Pelechano V, Jakob P, Steinmetz LM, Zenz T, Huber W. (2013)

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

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

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. doi: 10.1186/1471-2164-14-90
Europe PMC | doi

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):409-421. doi: 10.1016/j.molcel.2012.08.018
Europe PMC | doi

Hobson DJ, Wei W, Steinmetz LM, Svejstrup JQ. (2012)

RNA polymerase II collision interrupts convergent transcription

Mol. Cell 48(3):365-374. doi: 10.1016/j.molcel.2012.08.027
Europe PMC | doi

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):671-675. doi: 10.1126/science.1224350
Europe PMC | doi

Delhomme N, Padioleau I, Furlong EE, Steinmetz LM. (2012)

easyRNASeq: a bioconductor package for processing RNA-Seq data

Bioinformatics 28(19):2532-2533. doi: 10.1093/bioinformatics/bts477
Europe PMC | doi

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. doi: 10.1371/journal.pgen.1002958
Europe PMC | doi