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246 publications

Year 2018

PubMed DOI Crossref
Placental lncRNA Expression Is Associated With Prenatal Phthalate Exposure
Machtinger R, Zhong J, Mansur A, ..., Karlsson O, Baccarelli AA
- 163 (1) 116-122 [2018-05-01; online 2018-01-29]
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PubMed DOI Crossref
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies
Tramontano M, Andrejev S, Pruteanu M, ..., Typas A, Patil KR
Nat. Microbiol 3 (4) 514-522 [2018-04-00; online 2018-03-19]
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PubMed DOI Crossref
In Vivo Visualization of β-Cells by Targeting of GPR44
Eriksson O, Johnström P, Cselenyi Z, ..., Skrtic S, Korsgren O
Diabetes 67 (2) 182-192 [2018-02-00; online 2017-12-05]
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PubMed DOI Crossref
Evaluation of Post-Mortem Effects on Global Brain DNA Methylation and Hydroxymethylation
Sjöholm LK, Ransome Y, Ekström TJ, Karlsson O
Basic Clin Pharmacol Toxicol 122 (2) 208-213 [2018-02-00; online 2017-11-13]
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PubMed DOI Crossref
Neurological and neuropsychological effects of low and moderate prenatal alcohol exposure
Comasco E, Rangmar J, Eriksson UJ, Oreland L
Acta Physiol 222 (1) e12892 [2018-01-00; online 2017-05-30]
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PubMed DOI Crossref
Personality as an intermediate phenotype for genetic dissection of alcohol use disorder
Oreland L, Lagravinese G, Toffoletto S, ..., Robert Cloninger C, Comasco E
J Neural Transm 125 (1) 107-130 [2018-01-00; online 2017-01-04]
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Year 2017

PubMed DOI Crossref
Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds.
Wurzbacher C, Nilsson RH, Rautio M, Peura S
pmc
ISME J 11 (8) 1938-1941 [2017-08-00; online 2017-04-21]
Affiliated researcher Fellow
PubMed DOI Crossref
The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization
Alam MT, Olin-Sandoval V, Stincone A, ..., Luisi BF, Ralser M
Nat Commun 8 (-) 16018 [2017-07-10; online 2017-07-10]
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PubMed DOI Crossref
Quantification of HER2 and estrogen receptor heterogeneity in breast cancer by single-molecule RNA fluorescence in situ hybridization.
Annaratone L, Simonetti M, Wernersson E, ..., Sapino A, Crosetto N
pmc
Oncotarget 8 (12) 18680-18698 [2017-03-21; online 2017-04-21]
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PubMed DOI Crossref
Understanding the Role of GPCR Heteroreceptor Complexes in Modulating the Brain Networks in Health and Disease
Borroto-Escuela DO, Carlsson J, Ambrogini P, ..., Diaz-Cabiale Z, Fuxe K
Front. Cell. Neurosci. 11 (-) - [2017-02-21; online 2017-02-21]
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PubMed DOI Crossref
Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics
Janouškovec J, Gavelis GS, Burki F, ..., Rohwer FL, Saldarriaga JF
Proceedings of the National Academy of Sciences 114 (2) E171-E180 [2017-01-10; online 2016-12-27]
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Year 2016

PubMed DOI Crossref
Functional Metabolomics Describes the Yeast Biosynthetic Regulome
Mülleder M, Calvani E, Alam MT, ..., Zelezniak A, Ralser M
Cell 167 (2) 553-565.e12 [2016-10-00; online 2016-10-00]
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PubMed DOI Crossref
IFN-γ Hinders Recovery from Mucosal Inflammation during Antibiotic Therapy for Salmonella Gut Infection
Dolowschiak T, Mueller AA, Pisan LJ, ..., Mueller C, Hardt WD
Cell Host & Microbe 20 (2) 238-249 [2016-08-00; online 2016-08-00]
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PubMed DOI Crossref
An NK Cell Perforin Response Elicited via IL-18 Controls Mucosal Inflammation Kinetics during Salmonella Gut Infection
Müller AA, Dolowschiak T, Sellin ME, ..., LeibundGut-Landmann S, Hardt WD
PLoS Pathog 12 (6) e1005723 [2016-06-24; online 2016-06-24]
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PubMed DOI Crossref
The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons
García-Martínez J, Delgado-Ramos L, Ayala G, ..., Chávez S, Pérez-Ortín JE
Nucleic Acids Res 44 (8) 3643-3658 [2016-05-05; online 2015-12-29]
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PubMed DOI Crossref
Transcriptomics resources of human tissues and organs.
Uhlén M, Hallström BM, Lindskog C, ..., Pontén F, Nielsen J
pmc
Mol Syst Biol 12 (4) 862 [2016-04-04; online 2016-04-04]
Affiliated researcher Fellow
PubMed DOI Crossref
Evolutionary Origins of Rhizarian Parasites
Sierra R, Cañas-Duarte SJ, Burki F, ..., Arzul I, Pawlowski J
Molecular Biology and Evolution 33 (4) 980-983 [2016-04-00; online 2015-12-16]
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PubMed DOI Crossref
Glycation Reactivity of a Quorum-Sensing Signaling Molecule
Tsuchikama K, Gooyit M, Harris TL, ..., Kaufmann GF, Janda KD
Angewandte Chemie International Edition 55 (12) 4002-4006 [2016-03-14; online 2016-02-17]
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PubMed DOI Crossref
Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson’s disease revealed by deep sequencing analysis
Pantano L, Friedländer MR, Escaramís G, ..., Estivill X, Martí E
- 32 (5) 673-681 [2016-03-01; online 2015-11-02]
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PubMed DOI Crossref
Stepwise nucleosome translocation by RSC remodeling complexes
Harada BT, Hwang WL, Deindl S, ..., Bartholomew B, Zhuang X
- 5 (-) - [2016-02-19; online 2016-02-19]
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PubMed DOI Crossref
The metabolic background is a global player in Saccharomyces gene expression epistasis
Alam MT, Zelezniak A, Mülleder M, ..., Lilley KS, Ralser M
Nat. Microbiol 1 (3) 15030 [2016-02-01; online 2016-02-01]
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PubMed DOI Crossref
Genetic code expansion in stable cell lines enables encoded chromatin modification
Elsässer SJ, Ernst RJ, Walker OS, Chin JW
Nat Methods 13 (2) 158-164 [2016-02-00; online 2016-01-04]
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PubMed DOI Crossref
Photoactivation of Mutant Isocitrate Dehydrogenase 2 Reveals Rapid Cancer-Associated Metabolic and Epigenetic Changes
Walker OS, Elsässer SJ, Mahesh M, ..., Balasubramanian S, Chin JW
J. Am. Chem. Soc. 138 (3) 718-721 [2016-01-27; online 2016-01-12]
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Year 2015

PubMed DOI Crossref
Litomosoides sigmodontis: A jird urine metabolome study
Globisch D, Specht S, Pfarr KM, ..., Hoerauf A, Janda KD
Bioorganic & Medicinal Chemistry Letters 25 (24) 5804-5807 [2015-12-00; online 2015-12-00]
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PubMed DOI Crossref
Characterization of the honeybee AmNaV1 channel and tools to assess the toxicity of insecticides
Gosselin-Badaroudine P, Moreau A, Delemotte L, ..., Klein ML, Chahine M
Sci Rep 5 (1) - [2015-12-00; online 2015-07-23]
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DOI Crossref
The 2015 super-resolution microscopy roadmap
Hell SW, Sahl SJ, Bates M, ..., Diaspro A, Cordes T
J. Phys. D: Appl. Phys. 48 (44) 443001 [2015-11-11; online 2015-10-15]
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PubMed DOI Crossref
The gut microbiota modulates host amino acid and glutathione metabolism in mice.
Mardinoglu A, Shoaie S, Bergentall M, ..., Bäckhed F, Nielsen J
pmc
Mol Syst Biol 11 (10) 834 [2015-10-16; online 2015-10-16]
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PubMed DOI Crossref
Canine CNGA3 Gene Mutations Provide Novel Insights into Human Achromatopsia-Associated Channelopathies and Treatment
Tanaka N, Dutrow EV, Miyadera K, ..., Tanaka JC, Guziewicz KE
PLoS ONE 10 (9) e0138943 [2015-09-25; online 2015-09-25]
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PubMed DOI Crossref
Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives
Janouškovec J, Tikhonenkov DV, Burki F, ..., Mylnikov AP, Keeling PJ
Proceedings of the National Academy of Sciences 112 (33) 10200-10207 [2015-08-18; online 2015-02-25]
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PubMed DOI Crossref
Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory
Cournia Z, Allen TW, Andricioaei I, ..., Smith JC, Bondar AN
J Membrane Biol 248 (4) 611-640 [2015-08-00; online 2015-06-11]
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PubMed DOI Crossref
Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome
Shoaie S, Ghaffari P, Kovatcheva-Datchary P, ..., Bäckhed F, Nielsen J
Cell Metabolism 22 (2) 320-331 [2015-08-00; online 2015-08-00]
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PubMed DOI Crossref
Inflammasomes of the intestinal epithelium
Sellin ME, Maslowski KM, Maloy KJ, Hardt WD
Trends in Immunology 36 (8) 442-450 [2015-08-00; online 2015-08-00]
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PubMed DOI Crossref
Mitochondrial ribosome assembly in health and disease
De Silva D, Tu YT, Amunts A, Fontanesi F, Barrientos A
Cell Cycle 14 (14) 2226-2250 [2015-07-18; online 2015-06-00]
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PubMed DOI Crossref
Logical transformation of genome-scale metabolic models for gene level applications and analysis
Zhang C, Ji B, Mardinoglu A, Nielsen J, Hua Q
Bioinformatics 31 (14) 2324-2331 [2015-07-15; online 2015-03-02]
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PubMed DOI Crossref
Nutritional Control of DNA Replication Initiation through the Proteolysis and Regulated Translation of DnaA
Leslie DJ, Heinen C, Schramm FD, ..., Laub MT, Jonas K
PLoS Genet 11 (7) e1005342 [2015-07-02; online 2015-07-02]
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PubMed DOI Crossref
The Nuclear PolyA-Binding Protein Nab2p Is Essential for mRNA Production
Schmid M, Olszewski P, Pelechano V, ..., Steinmetz LM, Jensen TH
Cell Reports 12 (1) 128-139 [2015-07-00; online 2015-07-00]
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PubMed DOI Crossref
Critical Role of Histone Turnover in Neuronal Transcription and Plasticity
Maze I, Wenderski W, Noh KM, ..., Molina H, Allis CD
Neuron 87 (1) 77-94 [2015-07-00; online 2015-07-00]
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PubMed DOI Crossref
Comparative sequence analysis suggests a conserved gating mechanism for TRP channels
Palovcak E, Delemotte L, Klein ML, Carnevale V
J Gen Physiol 146 (1) 37-50 [2015-07-00; online 2015-06-15]
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PubMed DOI Crossref
Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus Are Established in the Endosperm
Rebernig CA, Lafon-Placette C, Hatorangan MR, Slotte T, Köhler C
PLoS Genet 11 (6) e1005295 [2015-06-18; online 2015-06-18]
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PubMed DOI Crossref
Single-cell polyadenylation site mapping reveals 3' isoform choice variability.
Velten L, Anders S, Pekowska A, ..., Pelechano V, Steinmetz LM
pmc GEO
Mol Syst Biol 11 (6) 812 [2015-06-03; online 2015-06-03]
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PubMed DOI Crossref
Widespread Co-translational RNA Decay Reveals Ribosome Dynamics
Pelechano V, Wei W, Steinmetz LM
Cell 161 (6) 1400-1412 [2015-06-00; online 2015-06-00]
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PubMed DOI Crossref
Metabolic dependencies drive species co-occurrence in diverse microbial communities
Zelezniak A, Andrejev S, Ponomarova O, ..., Bork P, Patil KR
Proceedings of the National Academy of Sciences 112 (20) 6449-6454 [2015-05-19; online 2015-05-04]
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PubMed DOI Crossref
Effect of predicted protein-truncating genetic variants on the human transcriptome
Rivas MA, Pirinen M, Conrad DF, ..., None , None
Science 348 (6235) 666-669 [2015-05-08; online 2015-05-07]
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PubMed DOI Crossref
The structure of the human mitochondrial ribosome
Amunts A, Brown A, Toots J, Scheres SHW, Ramakrishnan V
Science 348 (6230) 95-98 [2015-04-03; online 2015-04-02]
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PubMed DOI Crossref
Integrated genome and transcriptome sequencing of the same cell
Dey SS, Kester L, Spanjaard B, Bienko M, van Oudenaarden A
Nat Biotechnol 33 (3) 285-289 [2015-03-00; online 2015-01-19]
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PubMed DOI Crossref
Flagellin as Carrier and Adjuvant in Cocaine Vaccine Development
Lockner JW, Eubanks LM, Choi JL, ..., Wilson IA, Janda KD
Mol. Pharmaceutics 12 (2) 653-662 [2015-02-02; online 2015-01-07]
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PubMed DOI Crossref
Bactobolin A Binds to a Site on the 70S Ribosome Distinct from Previously Seen Antibiotics
Amunts A, Fiedorczuk K, Truong TT, ..., Greenberg EP, Ramakrishnan V
Journal of Molecular Biology 427 (4) 753-755 [2015-02-00; online 2015-02-00]
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PubMed DOI Crossref
Gating pore currents are defects in common with two Nav1.5 mutations in patients with mixed arrhythmias and dilated cardiomyopathy
Moreau A, Gosselin-Badaroudine P, Delemotte L, Klein ML, Chahine M
J Gen Physiol 145 (2) 93-106 [2015-02-00; online 2015-01-26]
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PubMed DOI Crossref
Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle
Jordán-Pla A, Gupta I, de Miguel-Jiménez L, ..., Pelechano V, Pérez-Ortín JE
- 43 (2) 787-802 [2015-01-30; online 2014-12-29]
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PubMed DOI Crossref
Dual Channel RESOLFT Nanoscopy by Using Fluorescent State Kinetics
Testa I, D’Este E, Urban NT, Balzarotti F, Hell SW
Nano Lett. 15 (1) 103-106 [2015-01-14; online 2014-12-02]
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PubMed DOI Crossref
A high-throughput ChIP-Seq for large-scale chromatin studies.
Chabbert CD, Adjalley SH, Klaus B, ..., Pelechano V, Steinmetz LM
pmc
Mol Syst Biol 11 (1) 777 [2015-01-12; online 2015-01-12]
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PubMed DOI Crossref
Free-energy landscape of ion-channel voltage-sensor–domain activation
Delemotte L, Kasimova MA, Klein ML, Tarek M, Carnevale V
Proceedings of the National Academy of Sciences 112 (1) 124-129 [2015-01-06; online 2014-12-22]
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PubMed DOI Crossref
Modulation of Bacterial Proliferation as a Survival Strategy
Heinrich K, Leslie DJ, Jonas K
- - (-) 127-171 [2015-00-00; online 2015-00-00]
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Year 2014

PubMed DOI Crossref
Toxicogenomics directory of chemically exposed human hepatocytes
Grinberg M, Stöber RM, Edlund K, ..., Rahnenführer J, Hengstler JG
Arch Toxicol 88 (12) 2261-2287 [2014-12-00; online 2014-11-16]
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PubMed DOI Crossref
Structure of the large ribosomal subunit from human mitochondria
Brown A, Amunts A, Bai Xc, ..., Scheres SHW, Ramakrishnan V
Science 346 (6210) 718-722 [2014-11-07; online 2014-10-02]
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PubMed DOI Crossref
High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface
Schmitt BM, Rudolph KLM, Karagianni P, ..., Marioni JC, Kutter C
Genome Res. 24 (11) 1797-1807 [2014-11-00; online 2014-08-13]
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PubMed DOI Crossref
Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways
Ballester B, Medina-Rivera A, Schmidt D, ..., Flicek P, Wilson MD
- 3 (-) - [2014-10-03; online 2014-10-03]
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PubMed DOI Crossref
Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders
Blanco S, Dietmann S, Flores JV, ..., Odom DT, Frye M
The EMBO Journal 33 (18) 2020-2039 [2014-09-17; online 2014-07-25]
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PubMed DOI Crossref
Antibiotic treatment selects for cooperative virulence of Salmonella typhimurium.
Diard M, Sellin ME, Dolowschiak T, ..., Ackermann M, Hardt WD
Curr. Biol. 24 (17) 2000-2005 [2014-09-08; online 2014-08-14]
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PubMed DOI Crossref
Evidence for the Retention of Two Evolutionary Distinct Plastids in Dinoflagellates with Diatom Endosymbionts
Hehenberger E, Imanian B, Burki F, Keeling PJ
- 6 (9) 2321-2334 [2014-09-00; online 2014-08-28]
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PubMed DOI Crossref
Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges
Kufareva I, Katritch V, Stevens RC, Abagyan R
Structure 22 (8) 1120-1139 [2014-08-00; online 2014-08-00]
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PubMed DOI Crossref
Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA
Hwang WL, Deindl S, Harada BT, Zhuang X
Nature 512 (7513) 213-217 [2014-08-00; online 2014-06-29]
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PubMed DOI Crossref
Genome-wide identification of transcript start and end sites by transcript isoform sequencing
Pelechano V, Wei W, Jakob P, Steinmetz LM
Nat Protoc 9 (7) 1740-1759 [2014-07-00; online 2014-06-26]
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PubMed DOI Crossref
Association of condensin with chromosomes depends on DNA binding by its HEAT-repeat subunits
Piazza I, Rutkowska A, Ori A, ..., Beck M, Haering CH
Nat Struct Mol Biol 21 (6) 560-568 [2014-06-00; online 2014-05-18]
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PubMed DOI Crossref
Proteome labeling and protein identification in specific tissues and at specific developmental stages in an animal
Elliott TS, Townsley FM, Bianco A, ..., Lilley KS, Chin JW
Nat Biotechnol 32 (5) 465-472 [2014-05-00; online 2014-04-13]
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DOI Crossref
Evidence of Conducting Hydrophobic Nanopores Across Membranes in Response to an Electric Field
Dehez F, Delemotte L, Kramar P, Miklavčič D, Tarek M
J. Phys. Chem. C 118 (13) 6752-6757 [2014-04-03; online 2014-03-19]
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PubMed DOI Crossref
Structure of the Yeast Mitochondrial Large Ribosomal Subunit
Amunts A, Brown A, Bai Xc, ..., Scheres SHW, Ramakrishnan V
Science 343 (6178) 1485-1489 [2014-03-28; online 2014-03-27]
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PubMed DOI Crossref
Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions
Gupta I, Clauder-Munster S, Klaus B, ..., Pelechano V, Steinmetz LM
Mol Syst Biol 10 (2) 719-719 [2014-03-20; online 2014-02-25]
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PubMed DOI Crossref
Two-Color RESOLFT Nanoscopy with Green and Red Fluorescent Photochromic Proteins
Lavoie-Cardinal F, Jensen NA, Westphal V, ..., Jakobs S, Hell SW
ChemPhysChem 15 (4) 655-663 [2014-03-17; online 2014-01-21]
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PubMed DOI Crossref
A Generic Method for Design of Oligomer-Specific Antibodies
Brännström K, Lindhagen-Persson M, Gharibyan AL, ..., Forsgren L, Olofsson A
PLoS ONE 9 (3) e90857 [2014-03-11; online 2014-03-11]
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PubMed DOI Crossref
Genetic Encoding of Photocaged Cysteine Allows Photoactivation of TEV Protease in Live Mammalian Cells
Nguyen DP, Mahesh M, Elsässer SJ, ..., Uttamapinant C, Chin JW
J. Am. Chem. Soc. 136 (6) 2240-2243 [2014-02-12; online 2014-01-30]
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PubMed DOI Crossref
Evolutionary imprint of activation: The design principles of VSDs
Palovcak E, Delemotte L, Klein ML, Carnevale V
J Gen Physiol 143 (2) 145-156 [2014-02-00; online 2014-01-27]
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PubMed DOI Crossref
Endosymbiotic Gene Transfer in Tertiary Plastid-Containing Dinoflagellates
Burki F, Imanian B, Hehenberger E, ..., Maruyama S, Keeling PJ
Eukaryotic Cell 13 (2) 246-255 [2014-02-00; online 2013-12-02]
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PubMed DOI Crossref
FuseFISH: Robust Detection of Transcribed Gene Fusions in Single Cells
Semrau S, Crosetto N, Bienko M, ..., Chiarle R, van Oudenaarden A
Cell Reports 6 (1) 18-23 [2014-01-00; online 2014-01-00]
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PubMed DOI Crossref
Dynamic remodeling of histone modifications in response to osmotic stress in Saccharomyces cerevisiae
Magraner-Pardo L, Pelechano V, Coloma M, Tordera V
BMC Genomics 15 (1) 247 [2014-00-00; online 2014-00-00]
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PubMed DOI Crossref
Characterisation of novel microRNAs in the Black flying fox (Pteropus alecto) by deep sequencing
Cowled C, Stewart CR, Likic VA, ..., Bean AG, Wang Lf
BMC Genomics 15 (1) 682 [2014-00-00; online 2014-00-00]
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PubMed DOI Crossref
Evidence for the biogenesis of more than 1,000 novel human microRNAs
Friedländer MR, Lizano E, Houben AJ, ..., Martí E, Estivill X
Genome Biol Genome Biology 15 (4) R57 [2014-00-00; online 2014-00-00]
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Year 2013

PubMed DOI Crossref
Understanding the interactions between bacteria in the human gut through metabolic modeling
Shoaie S, Karlsson F, Mardinoglu A, ..., Bordel S, Nielsen J
Sci Rep 3 (1) - [2013-12-00; online 2013-08-28]
Fellow
PubMed DOI Crossref
Gene regulation by antisense transcription
Pelechano V, Steinmetz LM
Nat Rev Genet 14 (12) 880-893 [2013-12-00; online 2013-11-12]
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PubMed DOI Crossref
Genome-scale modeling of human metabolism - a systems biology approach
Mardinoglu A, Gatto F, Nielsen J
Biotechnology Journal 8 (9) 985-996 [2013-09-00; online 2013-04-24]
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PubMed DOI Crossref
Hira-Dependent Histone H3.3 Deposition Facilitates PRC2 Recruitment at Developmental Loci in ES Cells
Banaszynski LA, Wen D, Dewell S, ..., Zheng D, Allis CD
Cell 155 (1) 107-120 [2013-09-00; online 2013-09-00]
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PubMed DOI Crossref
Phylogenomics of the Intracellular Parasite Mikrocytos mackini Reveals Evidence for a Mitosome in Rhizaria
Burki F, Corradi N, Sierra R, ..., Abbott CL, Keeling PJ
Current Biology 23 (16) 1541-1547 [2013-08-00; online 2013-08-00]
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PubMed DOI Crossref
Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality
Ntini E, Järvelin AI, Bornholdt J, ..., Sandelin A, Jensen TH
Nat Struct Mol Biol 20 (8) 923-928 [2013-08-00; online 2013-07-14]
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PubMed DOI Crossref
MicroRNA expression profiling in blood from fragile X-associated tremor/ataxia syndrome patients
Alvarez-Mora MI, Rodriguez-Revenga L, Madrigal I, ..., Estivill X, Milà M
- 12 (6) 595-603 [2013-08-00; online 2013-07-24]
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Structure-based Discovery of Antagonists of Nuclear Receptor LRH-1
Benod C, Carlsson J, Uthayaruban R, ..., Sablin EP, Fletterick RJ
J. Biol. Chem. 288 (27) 19830-19844 [2013-07-05; online 2013-05-10]
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PubMed DOI Crossref
Upregulation of a small vault RNA (svtRNA2-1a) is an early event in Parkinson disease and induces neuronal dysfunction.
Miñones-Moyano E, Friedländer MR, Pallares J, ..., Estivill X, Martí E
pmc
RNA Biol 10 (7) 1093-1106 [2013-07-00; online 2013-05-01]
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PubMed DOI Crossref
Structural Basis for Activation of ZAP-70 by Phosphorylation of the SH2-Kinase Linker
Yan Q, Barros T, Visperas PR, ..., Weiss A, Kuriyan J
Molecular and Cellular Biology 33 (11) 2188-2201 [2013-06-01; online 2013-03-25]
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PubMed DOI Crossref
Mechanistic Insights into the LsrK Kinase Required for Autoinducer-2 Quorum Sensing Activation
Zhu J, Hixon MS, Globisch D, Kaufmann GF, Janda KD
J. Am. Chem. Soc. 135 (21) 7827-7830 [2013-05-29; online 2013-05-16]
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PubMed DOI Crossref
Role of aspartate 132 at the orifice of a proton pathway in cytochrome c oxidase
Johansson AL, Hogbom M, Carlsson J, Gennis RB, Brzezinski P
Proceedings of the National Academy of Sciences 110 (22) 8912-8917 [2013-05-28; online 2013-05-14]
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PubMed DOI Crossref
Extensive transcriptional heterogeneity revealed by isoform profiling
Pelechano V, Wei W, Steinmetz LM
Nature 497 (7447) 127-131 [2013-04-24; online 2013-04-24]
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PubMed DOI Crossref
Conduction in a Biological Sodium Selective Channel
Stock L, Delemotte L, Carnevale V, Treptow W, Klein ML
J. Phys. Chem. B 117 (14) 3782-3789 [2013-04-11; online 2013-03-27]
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Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing.
Crosetto N, Mitra A, Silva MJ, ..., Rowicka M, Dikic I
pmc mid
Nat. Methods 10 (4) 361-365 [2013-04-00; online 2013-03-17]
Affiliated researcher Fellow
PubMed DOI Crossref
Global Gene Expression Profiling Reveals SPINK1 as a Potential Hepatocellular Carcinoma Marker
Marshall A, Lukk M, Kutter C, ..., Alexander G, Odom DT
PLoS ONE 8 (3) e59459 [2013-03-18; online 2013-03-18]
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PubMed DOI Crossref
Onchocerca volvulus-neurotransmitter tyramine is a biomarker for river blindness
Globisch D, Moreno AY, Hixon MS, ..., Hoerauf A, Janda KD
Proceedings of the National Academy of Sciences 110 (11) 4218-4223 [2013-03-12; online 2013-02-25]
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PubMed DOI Crossref
An efficient method for genome-wide polyadenylation site mapping and RNA quantification
Wilkening S, Pelechano V, Järvelin AI, ..., Benes V, Steinmetz LM
- 41 (5) e65-e65 [2013-03-01; online 2013-01-07]
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PubMed DOI Crossref
Proton Uptake and pKa Changes in the Uncoupled Asn139Cys Variant of Cytochrome c Oxidase
Johansson AL, Carlsson J, Högbom M, ..., Gennis RB, Brzezinski P
Biochemistry 52 (5) 827-836 [2013-02-05; online 2013-01-25]
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PubMed DOI Crossref
A versatile genome-scale PCR-based pipeline for high-definition DNA FISH
Bienko M, Crosetto N, Teytelman L, ..., Itzkovitz S, van Oudenaarden A
Nat Methods 10 (2) 122-124 [2013-02-00; online 2012-12-23]
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PubMed DOI Crossref
Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains
Hota SK, Bhardwaj SK, Deindl S, ..., Zhuang X, Bartholomew B
Nat Struct Mol Biol 20 (2) 222-229 [2013-02-00; online 2013-01-20]
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PubMed DOI Crossref
Unveiling Distribution Patterns of Freshwater Phytoplankton by a Next Generation Sequencing Based Approach
Eiler A, Drakare S, Bertilsson S, ..., Znachor P, Lindström ES
PLoS ONE 8 (1) e53516 [2013-01-22; online 2013-01-22]
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ISWI Remodelers Slide Nucleosomes with Coordinated Multi-Base-Pair Entry Steps and Single-Base-Pair Exit Steps
Deindl S, Hwang WL, Hota SK, ..., Bartholomew B, Zhuang X
Cell 152 (3) 442-452 [2013-01-00; online 2013-01-00]
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Latent Regulatory Potential of Human-Specific Repetitive Elements
Ward MC, Wilson MD, Barbosa-Morais NL, ..., Blencowe BJ, Odom DT
Molecular Cell 49 (2) 262-272 [2013-01-00; online 2013-01-00]
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Year 2012

PubMed DOI Crossref
The Evolutionary Landscape of Alternative Splicing in Vertebrate Species
Barbosa-Morais NL, Irimia M, Pan Q, ..., Frey BJ, Blencowe BJ
Science 338 (6114) 1587-1593 [2012-12-21; online 2012-12-20]
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Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs
Curtis BA, Tanifuji G, Burki F, ..., Grigoriev IV, Archibald JM
Nature 492 (7427) 59-65 [2012-12-00; online 2012-11-28]
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Gating pore currents and the resting state of Nav1.4 voltage sensor domains
Gosselin-Badaroudine P, Delemotte L, Moreau A, Klein ML, Chahine M
Proceedings of the National Academy of Sciences 109 (47) 19250-19255 [2012-11-20; online 2012-11-07]
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DAXX envelops a histone H3.3–H4 dimer for H3.3-specific recognition
Elsässer SJ, Huang H, Lewis PW, ..., Allis CD, Patel DJ
Nature 491 (7425) 560-565 [2012-11-00; online 2012-10-17]
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Mammalian SEPT9 isoforms direct microtubule-dependent arrangements of septin core heteromers
Sellin ME, Stenmark S, Gullberg M
MBoC 23 (21) 4242-4255 [2012-11-00; online 2012-11-00]
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Dual Effect of Phosphatidyl (4,5)-Bisphosphate PIP2on Shaker K+Channels
Abderemane-Ali F, Es-Salah-Lamoureux Z, Delemotte L, ..., Baró I, Loussouarn G
J. Biol. Chem. 287 (43) 36158-36167 [2012-10-19; online 2012-08-29]
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Low values of 5-hydroxymethylcytosine (5hmC), the “sixth base,” are associated with anaplasia in human brain tumors
Kraus TFJ, Globisch D, Wagner M, ..., Carell T, Kretzschmar HA
Int. J. Cancer 131 (7) 1577-1590 [2012-10-01; online 2012-03-02]
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Molecular-Level Characterization of Lipid Membrane Electroporation using Linearly Rising Current
Kramar P, Delemotte L, Maček Lebar A, ..., Tarek M, Miklavčič D
J Membrane Biol 245 (10) 651-659 [2012-10-00; online 2012-08-11]
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Intragenomic Spread of Plastid-Targeting Presequences in the Coccolithophore Emiliania huxleyi
Burki F, Hirakawa Y, Keeling PJ
- 29 (9) 2109-2112 [2012-09-00; online 2012-03-30]
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Nanoscopy of Living Brain Slices with Low Light Levels
Testa I, Urban NT, Jakobs S, ..., Willig KI, Hell SW
Neuron 75 (6) 992-1000 [2012-09-00; online 2012-09-00]
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Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1
Peura S, Eiler A, Bertilsson S, ..., Tiirola M, Jones RI
ISME J 6 (9) 1640-1652 [2012-09-00; online 2012-03-15]
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The Revised Classification of Eukaryotes
Adl SM, Simpson AGB, Lane CE, ..., Smirnov A, Spiegel FW
J. Eukaryot. Microbiol. 59 (5) 429-514 [2012-09-00; online 2012-09-28]
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Genome-wide polyadenylation site mapping.
Pelechano V, Wilkening S, Järvelin AI, Tekkedil MM, Steinmetz LM
Meth. Enzymol. 513 (-) 271-296 [2012-08-30; online 2012-08-30]
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Large-Scale Identification of MicroRNA Targets in Murine Dgcr8-Deficient Embryonic Stem Cell Lines
Davis MPA, Abreu-Goodger C, van Dongen S, ..., Enright AJ, Dunham I
PLoS ONE 7 (8) e41762 [2012-08-17; online 2012-08-17]
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Phosphorylation of histone H3 Ser10 establishes a hierarchy for subsequent intramolecular modification events
Liokatis S, Stützer A, Elsässer SJ, ..., Fischle W, Selenko P
Nat Struct Mol Biol 19 (8) 819-823 [2012-08-00; online 2012-07-15]
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Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression
Kutter C, Watt S, Stefflova K, ..., Odom DT, Marques AC
PLoS Genet 8 (7) e1002841 [2012-07-26; online 2012-07-26]
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Rrp6p Controls mRNA Poly(A) Tail Length and Its Decoration with Poly(A) Binding Proteins
Schmid M, Poulsen MB, Olszewski P, ..., Moore C, Jensen TH
Molecular Cell 47 (2) 267-280 [2012-07-00; online 2012-07-00]
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The CDK5 repressor CDK5RAP1 is a methylthiotransferase acting on nuclear and mitochondrial RNA
Reiter V, Matschkal DMS, Wagner M, ..., Müller M, Carell T
- 40 (13) 6235-6240 [2012-07-00; online 2012-03-15]
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Collodictyon--An Ancient Lineage in the Tree of Eukaryotes
Zhao S, Burki F, Brate J, ..., Klaveness D, Shalchian-Tabrizi K
Molecular Biology and Evolution 29 (6) 1557-1568 [2012-06-01; online 2012-01-06]
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Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT
Agren R, Bordel S, Mardinoglu A, ..., Nookaew I, Nielsen J
PLoS Comput Biol 8 (5) e1002518 [2012-05-17; online 2012-05-17]
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Genetic architecture and adaptive significance of the selfing syndrome in Capsella.
Slotte T, Hazzouri KM, Stern D, Andolfatto P, Wright SI
pmc mid
Evolution 66 (5) 1360-1374 [2012-05-00; online 2012-03-03]
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Role of cis-12-Oxo-Phytodienoic Acid in Tomato Embryo Development
Goetz S, Hellwege A, Stenzel I, ..., Wasternack C, Hause B
PLANT PHYSIOLOGY 158 (4) 1715-1727 [2012-04-01; online 2012-02-14]
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Systems medicine and metabolic modelling.
Mardinoglu A, Nielsen J
J. Intern. Med. 271 (2) 142-154 [2012-02-00; online 2011-12-07]
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Select microRNAs are essential for early development in the sea urchin
Song JL, Stoeckius M, Maaskola J, ..., Rajewsky N, Wessel GM
Developmental Biology 362 (1) 104-113 [2012-02-00; online 2012-02-00]
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miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades
Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N
- 40 (1) 37-52 [2012-01-00; online 2011-09-10]
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Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
Schmidt D, Schwalie PC, Wilson MD, ..., Flicek P, Odom DT
Cell 148 (1-2) 335-348 [2012-01-00; online 2012-01-00]
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Re-evaluating the Green versus Red Signal in Eukaryotes with Secondary Plastid of Red Algal Origin
Burki F, Flegontov P, Oborník M, ..., Lukeš J, Keeling PJ
- 4 (6) 626-635 [2012-00-00; online 2012-05-16]
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Year 2011

PubMed DOI Crossref
Microtubules support a disk-like septin arrangement at the plasma membrane of mammalian cells
Sellin ME, Holmfeldt P, Stenmark S, Gullberg M
MBoC 22 (23) 4588-4601 [2011-12-00; online 2011-12-00]
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The Conserved Foot Domain of RNA Pol II Associates with Proteins Involved in Transcriptional Initiation and/or Early Elongation
García-López MC, Pelechano V, Mirón-García MC, ..., Pérez-Ortín JE, Navarro F
Genetics 189 (4) 1235-1248 [2011-12-00; online 2011-09-27]
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Mechanistic insights into the activation of oncogenic forms of EGF receptor
Wang Z, Longo PA, Tarrant MK, ..., Leahy DJ, Cole PA
Nat Struct Mol Biol 18 (12) 1388-1393 [2011-12-00; online 2011-11-20]
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Ligand discovery from a dopamine D3 receptor homology model and crystal structure
Carlsson J, Coleman RG, Setola V, ..., Roth BL, Shoichet BK
Nat Chem Biol 7 (11) 769-778 [2011-11-00; online 2011-09-18]
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Systems-Based Analysis of Modified tRNA Bases
Globisch D, Pearson D, Hienzsch A, ..., Sieber SA, Carell T
Angewandte Chemie International Edition 50 (41) 9739-9742 [2011-10-04; online 2011-08-31]
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Diffraction-unlimited all-optical imaging and writing with a photochromic GFP
Grotjohann T, Testa I, Leutenegger M, ..., Jakobs S, Hell SW
Nature 478 (7368) 204-208 [2011-10-00; online 2011-09-11]
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Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes
Kutter C, Brown GD, Gonçalves Â, ..., White RJ, Odom DT
Nat Genet 43 (10) 948-955 [2011-10-00; online 2011-08-28]
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A reversibly photoswitchable GFP-like protein with fluorescence excitation decoupled from switching
Brakemann T, Stiel AC, Weber G, ..., Hell SW, Jakobs S
Nat Biotechnol 29 (10) 942-947 [2011-10-00; online 2011-09-11]
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Deciphering the rules governing assembly order of mammalian septin complexes
Sellin ME, Sandblad L, Stenmark S, Gullberg M
MBoC 22 (17) 3152-3164 [2011-09-00; online 2011-09-00]
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Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment
Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R
Structure 19 (8) 1108-1126 [2011-08-00; online 2011-08-00]
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A genomic view of mRNA turnover in yeast
Pérez-Ortín JE, Jordán-Pla A, Pelechano V
Comptes Rendus Biologies 334 (8-9) 647-654 [2011-08-00; online 2011-08-00]
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5-Hydroxymethylcytosine, the Sixth Base of the Genome
Münzel M, Globisch D, Carell T
Angewandte Chemie International Edition 50 (29) 6460-6468 [2011-07-11; online 2011-06-17]
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Functional consequences of bidirectional promoters
Wei W, Pelechano V, Järvelin AI, Steinmetz LM
Trends in Genetics 27 (7) 267-276 [2011-07-00; online 2011-07-00]
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Discovery and Synthesis of New UV-Induced Intrastrand C(4−8)G and G(8−4)C Photolesions
Münzel M, Szeibert C, Glas AF, Globisch D, Carell T
J. Am. Chem. Soc. 133 (14) 5186-5189 [2011-04-13; online 2011-04-13]
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The RACK1 Signaling Scaffold Protein Selectively Interacts with Yersinia pseudotuberculosis Virulence Function
Thorslund SE, Edgren T, Pettersson J, ..., Wolf-Watz H, Fällman M
PLoS ONE 6 (2) e16784 [2011-02-10; online 2011-02-10]
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Reduced Efficacy of Natural Selection on Codon Usage Bias in Selfing Arabidopsis and Capsella Species
Qiu S, Zeng K, Slotte T, Wright S, Charlesworth D
- 3 (-) 868-880 [2011-01-01; online 2011-08-18]
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LC-MS based quantification of 2′-ribosylated nucleosides Ar(p) and Gr(p) in tRNA
Pearson D, Hienzsch A, Wagner M, ..., Özden D, Carell T
Chem. Commun. 47 (18) 5196 [2011-00-00; online 2011-00-00]
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Year 2010

PubMed DOI Crossref
Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates
Globisch D, Münzel M, Müller M, ..., Biel M, Carell T
PLoS ONE 5 (12) e15367 [2010-12-23; online 2010-12-23]
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PubMed DOI Crossref
Efficient Synthesis of 5-Hydroxymethylcytosine Containing DNA
Münzel M, Globisch D, Trindler C, Carell T
Org. Lett. 12 (24) 5671-5673 [2010-12-17; online 2010-12-17]
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A Complete Set of Nascent Transcription Rates for Yeast Genes
Pelechano V, Chávez S, Pérez-Ortín JE
PLoS ONE 5 (11) e15442 [2010-11-16; online 2010-11-16]
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A Novel Synthetic Route for the Anti-HIV Drug MC-1220 and its Analogues
Loksha YM, Globisch D, Loddo R, ..., La Colla P, Pedersen EB
ChemMedChem 5 (11) 1847-1849 [2010-11-08; online 2010-08-16]
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Far-Field Autofluorescence Nanoscopy
Bierwagen J, Testa I, Fölling J, ..., Eggeling C, Hell SW
Nano Lett. 10 (10) 4249-4252 [2010-10-13; online 2010-10-13]
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The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors
Rodríguez-Gil A, García-Martínez J, Pelechano V, ..., Pérez-Ortín JE, Chávez S
- 38 (14) 4651-4664 [2010-08-00; online 2010-04-10]
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DOI Crossref
Impacts of added dissolved organic carbon on boreal freshwater pelagic metabolism and food webs in mesocosm experiments
Kankaala P, Peura S, Nykänen H, ..., Tiirola M, Jones RI
Fund. App. Lim. 177 (3) 161-176 [2010-07-09; online 2010-07-09]
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Quantification of the Sixth DNA Base Hydroxymethylcytosine in the Brain
Münzel M, Globisch D, Brückl T, ..., Biel M, Carell T
Angewandte Chemie International Edition 49 (31) 5375-5377 [2010-06-25; online 2010-06-25]
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Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding
Schmidt D, Wilson MD, Ballester B, ..., Flicek P, Odom DT
Science 328 (5981) 1036-1040 [2010-05-21; online 2010-04-08]
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Structure-Based Discovery of A2A Adenosine Receptor Ligands
Carlsson J, Yoo L, Gao ZG, ..., Shoichet BK, Jacobson KA
J. Med. Chem. 53 (9) 3748-3755 [2010-05-13; online 2010-05-13]
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Understanding biological dynamics: following cells and molecules to track functions and mechanisms
Palamidessi A, Testa I, Frittoli E, ..., Scita G, Faretta M
Eur Biophys J 39 (6) 947-957 [2010-05-00; online 2009-05-20]
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Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes
Zelezniak A, Pers TH, Soares S, Patti ME, Patil KR
PLoS Comput Biol 6 (4) e1000729 [2010-04-01; online 2010-04-01]
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There is a steady-state transcriptome in exponentially growing yeast cells
Pelechano V, Pérez-Ortín JE
Yeast 27 (7) 413-422 [2010-03-17; online 2010-03-17]
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Intersubunit capture of regulatory segments is a component of cooperative CaMKII activation
Chao LH, Pellicena P, Deindl S, ..., Schulman H, Kuriyan J
Nat Struct Mol Biol 17 (3) 264-272 [2010-03-00; online 2010-02-07]
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Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions
Goldberg AD, Banaszynski LA, Noh KM, ..., Zheng D, Allis CD
Cell 140 (5) 678-691 [2010-03-00; online 2010-03-00]
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Regulation of Translesion Synthesis DNA Polymerase η by Monoubiquitination
Bienko M, Green CM, Sabbioneda S, ..., Lehmann AR, Dikic I
Molecular Cell 37 (3) 396-407 [2010-02-00; online 2010-02-00]
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Complex regulatory network encompassing the Csr, c-di-GMP and motility systems of Salmonella Typhimurium.
Jonas K, Edwards AN, Ahmad I, ..., Römling U, Melefors O
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Environ. Microbiol. 12 (2) 524-540 [2010-02-00; online 2009-11-17]
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Structure Determination and Improved Model of Plant Photosystem I
Amunts A, Toporik H, Borovikova A, Nelson N
J. Biol. Chem. 285 (5) 3478-3486 [2010-01-29; online 2009-11-18]
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Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists
Burki F, Kudryavtsev A, Matz MV, ..., Keeling PJ, Pawlowski J
BMC Evol Biol BMC Evolutionary Biology 10 (1) 377 [2010-00-00; online 2010-00-00]
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Deciphering the porcine intestinal microRNA transcriptome
Sharbati S, Friedlander MR, Sharbati J, ..., Rajewsky N, Einspanier R
BMC Genomics 11 (1) 275 [2010-00-00; online 2010-00-00]
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