Publications by authors named "Lars M Steinmetz"

100Publications

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

Elife 2020 Nov 23;9. Epub 2020 Nov 23.

Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.7554/eLife.60188DOI Listing
November 2020

iPSC Modeling of RBM20-Deficient DCM Identifies Upregulation of RBM20 as a Therapeutic Strategy.

Cell Rep 2020 Sep;32(10):108117

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany; Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA, USA; Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA; DZHK: German Center for Cardiovascular Research, Partner Site EMBL Heidelberg, Heidelberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.108117DOI Listing
September 2020

TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes.

Nucleic Acids Res 2020 10;48(18):e104

SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna, Sweden.

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http://dx.doi.org/10.1093/nar/gkaa691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7544212PMC
October 2020

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

Nat Protoc 2020 09 14;15(9):3009-3029. Epub 2020 Aug 14.

Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1038/s41596-020-0361-1DOI Listing
September 2020

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

Nat Methods 2020 06 1;17(6):629-635. Epub 2020 Jun 1.

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.

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http://dx.doi.org/10.1038/s41592-020-0837-5DOI Listing
June 2020

A Circulating Bioreactor Reprograms Cancer Cells Toward a More Mesenchymal Niche.

Adv Biosyst 2020 02 14;4(2):e1900139. Epub 2020 Jan 14.

Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA.

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http://dx.doi.org/10.1002/adbi.201900139DOI Listing
February 2020

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

Nat Cell Biol 2020 01 23;22(1):38-48. Epub 2019 Dec 23.

Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany.

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http://dx.doi.org/10.1038/s41556-019-0439-6DOI Listing
January 2020

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

Genome Res 2019 12 18;29(12):1974-1984. Epub 2019 Nov 18.

SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden.

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http://dx.doi.org/10.1101/gr.243378.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6886497PMC
December 2019

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

Biochim Biophys Acta Mol Basis Dis 2020 03 13;1866(3):165588. Epub 2019 Nov 13.

Glycometabolic Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, Saitama 351-0198, Japan; Suzuki Project, T-CiRA Joint Program, Fujisawa, Kanagawa 251-8555, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bbadis.2019.165588DOI Listing
March 2020

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

Proc Natl Acad Sci U S A 2019 04 16;116(18):8995-9001. Epub 2019 Apr 16.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305;

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http://dx.doi.org/10.1073/pnas.1902649116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6500157PMC
April 2019

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

Science 2019 04 28;364(6437):289-292. Epub 2019 Feb 28.

Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

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http://www.sciencemag.org/lookup/doi/10.1126/science.aav9973
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http://dx.doi.org/10.1126/science.aav9973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7301308PMC
April 2019

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency.

Cell Syst 2018 11 7;7(5):482-495.e10. Epub 2018 Nov 7.

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, Heidelberg 69117, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S24054712183038
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http://dx.doi.org/10.1016/j.cels.2018.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327227PMC
November 2018

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

FEBS J 2018 09 27;285(18):3376-3401. Epub 2018 Aug 27.

Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.

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http://dx.doi.org/10.1111/febs.14631DOI Listing
September 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 2018 12 2;28(6):946-960.e6. Epub 2018 Aug 2.

INSERM, U1016, Cochin Institute, 75014 Paris, France; CNRS, UMR8104, Cochin Institute, 75014 Paris, France; Paris Descartes University, Sorbonne Paris Cité, 75014 Paris, France; Assistance Publique Hôpitaux de Paris, Service de Diabétologie, Cochin Hospital, 75014 Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.cmet.2018.07.007DOI Listing
December 2018

Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol.

G3 (Bethesda) 2018 01 4;8(1):79-89. Epub 2018 Jan 4.

Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany

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http://dx.doi.org/10.1534/g3.117.300257DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765368PMC
January 2018

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

Methods Mol Biol 2018 ;1689:177-194

SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden.

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http://dx.doi.org/10.1007/978-1-4939-7380-4_16DOI Listing
May 2018

Genome Dynamics of Hybrid During Vegetative and Meiotic Divisions.

G3 (Bethesda) 2017 11 6;7(11):3669-3679. Epub 2017 Nov 6.

School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum 695016, India

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http://dx.doi.org/10.1534/g3.117.1135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5677154PMC
November 2017

Assembly of functionally integrated human forebrain spheroids.

Nature 2017 05 26;545(7652):54-59. Epub 2017 Apr 26.

Department of Psychiatry and Behavioral Sciences, Center for Sleep Sciences and Medicine, Stanford University School of Medicine, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/nature22330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805137PMC
May 2017

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

Nature 2017 04 5;544(7649):245-249. Epub 2017 Apr 5.

Department of Pathology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/nature21722DOI Listing
April 2017

Modulating Crossover Frequency and Interference for Obligate Crossovers in Meiosis.

G3 (Bethesda) 2017 05 5;7(5):1511-1524. Epub 2017 May 5.

School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Trivandrum 695016, India

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http://g3journal.org/lookup/doi/10.1534/g3.117.040071
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http://dx.doi.org/10.1534/g3.117.040071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5427503PMC
May 2017

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

Nucleic Acids Res 2017 04;45(7):3752-3766

Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, Vienna (BOKU), UFT-Campus Tulln, Konrad Lorenz Strasse 24, 3430 Tulln, Austria.

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http://dx.doi.org/10.1093/nar/gkw1292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397147PMC
April 2017

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

Nat Commun 2016 11 28;7:13534. Epub 2016 Nov 28.

Department of Life Science, Ewha Womans University, Seoul 03760, Korea.

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http://dx.doi.org/10.1038/ncomms13534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133700PMC
November 2016

A privacy-preserving solution for compressed storage and selective retrieval of genomic data.

Genome Res 2016 12 27;26(12):1687-1696. Epub 2016 Oct 27.

School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1101/gr.206870.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131820PMC
December 2016

SYGNALing a Red Light for Glioblastoma.

Cell Syst 2016 08;3(2):118-120

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA; Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.08.002DOI Listing
August 2016

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

G3 (Bethesda) 2016 08 9;6(8):2255-63. Epub 2016 Aug 9.

Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai 600036, India

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http://dx.doi.org/10.1534/g3.116.029900DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978881PMC
August 2016

Protein Abundance Control by Non-coding Antisense Transcription.

Cell Rep 2016 06 9;15(12):2625-36. Epub 2016 Jun 9.

Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Electronic address:

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http://www.cell.com/cell-reports/pdf/S2211-1247(16)30626-X.p
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http://www.cell.com/cms/attachment/2059509676/2062351064/mmc
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http://linkinghub.elsevier.com/retrieve/pii/S221112471630626
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http://dx.doi.org/10.1016/j.celrep.2016.05.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920891PMC
June 2016

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

Cell Rep 2016 05 12;15(8):1782-94. Epub 2016 May 12.

Department of Microbiology and Molecular Medicine, Faculty of Medicine, Institute of Genetics and Genomics, University of Geneva, 1211 Geneva 4, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.04.055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4880543PMC
May 2016

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

PeerJ 2016 26;4:e1981. Epub 2016 Apr 26.

Genome Biology Unit, European Molecular Biology Laboratory , Heidelberg , Germany.

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http://dx.doi.org/10.7717/peerj.1981DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860309PMC
May 2016

Sensing a revolution.

Mol Syst Biol 2016 Apr 26;12(4):867. Epub 2016 Apr 26.

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848763PMC
http://dx.doi.org/10.15252/msb.20166873DOI Listing
April 2016

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

Genome Biol 2016 Mar 8;17:45. Epub 2016 Mar 8.

Stanford Genome Technology Center, Department of Biochemistry, Stanford University, 3165 Porter Drive, Palo Alto, CA, 94304, USA.

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http://dx.doi.org/10.1186/s13059-016-0900-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784398PMC
March 2016

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

Cell Rep 2016 Mar 3;14(10):2463-75. Epub 2016 Mar 3.

Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Stanford Genome Technology Center, Palo Alto, CA 94304, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.02.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4806524PMC
March 2016

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

Nat Protoc 2016 Feb 28;11(2):359-76. Epub 2016 Jan 28.

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.

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http://dx.doi.org/10.1038/nprot.2016.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4732566PMC
February 2016

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

Cell Rep 2015 Nov 12;13(8):1610-22. Epub 2015 Nov 12.

Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.10.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4662874PMC
November 2015

Integrating Cell Phone Imaging with Magnetic Levitation (i-LEV) for Label-Free Blood Analysis at the Point-of-Living.

Small 2016 Mar 2;12(9):1222-1229. Epub 2015 Nov 2.

Canary Center at Stanford for Cancer Early Detection, Radiology Department, School of Medicine, Stanford University, CA, USA, 94304.

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http://dx.doi.org/10.1002/smll.201501845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775401PMC
March 2016

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

Methods Mol Biol 2016 ;1358:295-302

Genome Biology Unit, EMBL Heidelberg, Heidelberg, Germany.

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http://dx.doi.org/10.1007/978-1-4939-3067-8_18DOI Listing
July 2016

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

Methods Mol Biol 2016 ;1358:131-9

European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.

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http://dx.doi.org/10.1007/978-1-4939-3067-8_8DOI Listing
July 2016

Inflammation-Induced Emergency Megakaryopoiesis Driven by Hematopoietic Stem Cell-like Megakaryocyte Progenitors.

Cell Stem Cell 2015 Oct 20;17(4):422-34. Epub 2015 Aug 20.

Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Division of Stem Cells and Cancer, Hematopoietic Stem Cells and Stress Group, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2015.07.007DOI Listing
October 2015

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

Nat Immunol 2015 Sep 3;16(9):933-41. Epub 2015 Aug 3.

1] Department of Genetics, Stanford University, School of Medicine, California, USA. [2] Stanford Genome Technology Center, Stanford University, California, USA. [3] European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.

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http://dx.doi.org/10.1038/ni.3246DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675844PMC
September 2015

Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics.

Proc Natl Acad Sci U S A 2015 Aug 20;112(32):E4354-63. Epub 2015 Jul 20.

Demirci Bio-Acoustic-Microelectromechanical Systems in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Radiology Department, Stanford University School of Medicine, Palo Alto, CA 94304; Department of Electrical Engineering (By courtesy), Stanford University, Stanford, CA 94305

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http://dx.doi.org/10.1073/pnas.1510824112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538635PMC
August 2015

Magnetic levitation of single cells.

Proc Natl Acad Sci U S A 2015 Jul 29;112(28):E3661-8. Epub 2015 Jun 29.

Canary Center at Stanford for Cancer Early Detection, Radiology Department, School of Medicine, Stanford University, Stanford, CA 94304;

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http://dx.doi.org/10.1073/pnas.1509250112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4507238PMC
July 2015

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

Cell Rep 2015 Jul 25;12(1):128-139. Epub 2015 Jun 25.

Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, 8000 Aarhus C., Denmark. Electronic address:

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http://www.cell.com/cell-reports/pdf/S2211-1247(15)00606-3.p
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http://linkinghub.elsevier.com/retrieve/pii/S221112471500606
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http://dx.doi.org/10.1016/j.celrep.2015.06.008DOI Listing
July 2015

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics.

Cell 2015 Jun;161(6):1400-12

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA; Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.05.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461875PMC
June 2015

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

Mol Syst Biol 2015 Jun 3;11(6):812. Epub 2015 Jun 3.

European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany Stanford Genome Technology Center, Palo Alto, CA, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4501847PMC
http://dx.doi.org/10.15252/msb.20156198DOI Listing
June 2015

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

PLoS Genet 2015 Jun 3;11(6):e1005195. Epub 2015 Jun 3.

Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India.

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http://dx.doi.org/10.1371/journal.pgen.1005195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4454590PMC
June 2015

Negative feedback buffers effects of regulatory variants.

Mol Syst Biol 2015 Jan 29;11(1):785. Epub 2015 Jan 29.

Computational Genomics, Gene Center, Ludwig Maximilians University, Munich, Germany

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332157PMC
http://dx.doi.org/10.15252/msb.20145844DOI Listing
January 2015

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

Mol Syst Biol 2015 Jan 12;11(1):777. Epub 2015 Jan 12.

European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany Stanford Genome Technology Center, Palo Alto, CA, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332152PMC
http://dx.doi.org/10.15252/msb.20145776DOI Listing
January 2015

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

Nucleic Acids Res 2015 Jan 29;43(2):787-802. Epub 2014 Dec 29.

Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain

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http://dx.doi.org/10.1093/nar/gku1349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333398PMC
January 2015

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

Nat Commun 2014 Dec 18;5:5585. Epub 2014 Dec 18.

1] European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany [2] Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA [3] Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1038/ncomms6585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4284804PMC
December 2014

Roadblock termination by reb1p restricts cryptic and readthrough transcription.

Mol Cell 2014 Dec;56(5):667-80

Centre de Génétique Moléculaire, CNRS UPR3404, 91190 Gif sur Yvette, France. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.10.026DOI Listing
December 2014

Variation in crossover frequencies perturb crossover assurance without affecting meiotic chromosome segregation in Saccharomyces cerevisiae.

Genetics 2015 Feb 2;199(2):399-412. Epub 2014 Dec 2.

School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Trivandrum 695016, India

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http://dx.doi.org/10.1534/genetics.114.172320DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317650PMC
February 2015

Ultrasensitive proteome analysis using paramagnetic bead technology.

Mol Syst Biol 2014 Oct 30;10:757. Epub 2014 Oct 30.

European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299378PMC
http://dx.doi.org/10.15252/msb.20145625DOI Listing
October 2014

High-density tiling microarray analysis of the full transcriptional activity of yeast.

Methods Mol Biol 2014 ;1205:257-73

Department of Animal Sciences, R.H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.

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http://dx.doi.org/10.1007/978-1-4939-1363-3_16DOI Listing
May 2015

A genome-wide map of mitochondrial DNA recombination in yeast.

Genetics 2014 Oct 31;198(2):755-71. Epub 2014 Jul 31.

European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany Stanford Genome Technology Center, Palo Alto, California 94304 Department of Genetics, Stanford University School of Medicine, Stanford, California 94305

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http://dx.doi.org/10.1534/genetics.114.166637DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196626PMC
October 2014

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

Nat Protoc 2014 Jul 26;9(7):1740-59. Epub 2014 Jun 26.

1] European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany. [2] Stanford Genome Technology Center, Palo Alto, California, USA. [3] Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.

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http://dx.doi.org/10.1038/nprot.2014.121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4111111PMC
July 2014

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

Genome Res 2014 Aug 13;24(8):1363-70. Epub 2014 May 13.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S3E1, Canada;

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http://dx.doi.org/10.1101/gr.170506.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4120089PMC
August 2014

Control of Cdc28 CDK1 by a stress-induced lncRNA.

Mol Cell 2014 Feb 6;53(4):549-61. Epub 2014 Feb 6.

Cell Signaling Unit, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.01.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4148690PMC
February 2014

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

Nucleic Acids Res 2014 Apr 4;42(7):4348-62. Epub 2014 Feb 4.

Department of Cell Biology and NCCR "Frontiers in Genetics", iGE3, University of Geneva, 1211 Geneva, Switzerland, EBI-EMBL Hinxton, Cambridge CB101SD, England, European Molecular Biology Laboratory, 69117 Heidelberg, Germany, Department of Genetics, Stanford University, Stanford, CA 94395 USA and Stanford Genome Technology Center, Palo Alto, CA 94303, USA.

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http://dx.doi.org/10.1093/nar/gku100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985671PMC
April 2014

Yeast growth plasticity is regulated by environment-specific multi-QTL interactions.

G3 (Bethesda) 2014 Jan 28;4(5):769-77. Epub 2014 Jan 28.

Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India

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http://dx.doi.org/10.1534/g3.113.009142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4025475PMC
January 2014

Gene regulation by antisense transcription.

Nat Rev Genet 2013 Dec 12;14(12):880-93. Epub 2013 Nov 12.

Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nrg3594DOI Listing
December 2013

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

Mol Syst Biol 2013 Oct 8;9:695. Epub 2013 Oct 8.

Laboratoire de Biologie Moléculaire de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Lyon, France.

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http://dx.doi.org/10.1038/msb.2013.53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817403PMC
October 2013

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

Proc Natl Acad Sci U S A 2013 Sep 3;110(38):15377-82. Epub 2013 Sep 3.

Genome Biology Unit and Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1073/pnas.1307202110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3780897PMC
September 2013

Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality.

Nat Struct Mol Biol 2013 Aug 14;20(8):923-8. Epub 2013 Jul 14.

Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.

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http://dx.doi.org/10.1038/nsmb.2640DOI Listing
August 2013

Extensive transcriptional heterogeneity revealed by isoform profiling.

Nature 2013 May 24;497(7447):127-31. Epub 2013 Apr 24.

Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature12121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705217PMC
May 2013

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

Mol Biol Evol 2013 Jul 14;30(7):1514-26. Epub 2013 Apr 14.

Department of Animal Sciences, Hebrew University of Jerusalem, Rehovot, Israel.

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http://dx.doi.org/10.1093/molbev/mst071DOI Listing
July 2013

Genotyping 1000 yeast strains by next-generation sequencing.

BMC Genomics 2013 Feb 9;14:90. Epub 2013 Feb 9.

Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany.

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http://dx.doi.org/10.1186/1471-2164-14-90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575377PMC
February 2013