Publications 2020

PubMed DOI Crossref

5´XP sRNA-seq: efficient identification of transcripts with and without 5´ phosphorylation reveals evolutionary conserved small RNA.

Kugelberg U, Nätt D, Skog S, Kutter C, Öst A

RNA Biol - (-) 1-12 [2020-12-31; online 2020-12-31]

Claudia Kutter Fellows programme

PubMed DOI Crossref

Ancient microRNA profiles of a 14,300-year-old canid samples confirm taxonomic origin and give glimpses into tissue-specific gene regulation from the Pleistocene.

Fromm B, Tarbier M, Smith O, ..., Gilbert TP, Friedlander MR

RNA - (-) - [2020-12-15; online 2020-12-15]

Fellows programme Marc Friedländer

PubMed DOI Crossref

Automated Removal of Non-homologous Sequence Stretches with PREQUAL.

Irisarri I, Burki F, Whelan S

Methods in molecular biology (Clifton, N.J.) 2231 (-) 147-162 [2020-12-09; online 2020-12-09]

Fabien Burki Fellows programme

PubMed DOI Crossref

Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development.

Malkani S, Chin CR, Cekanaviciute E, ..., Mason CE, Beheshti A

Cell Reports 33 (10) 108448 [2020-12-08; online 2020-11-25]

Fellows programme Marc Friedländer

PubMed DOI Crossref

Recent advances in single-molecule fluorescence microscopy render structural biology dynamic

Bacic L, Sabantsev A, Deindl S

Current Opinion in Structural Biology 65 (-) 61-68 [2020-12-00; online 2020-12-00]

Fellows programme Sebastian Deindl

PubMed DOI Crossref

Genome-wide detection of DNA double-strand breaks by in-suspension BLISS.

Bouwman BAM, Agostini F, Garnerone S, ..., Roukos V, Crosetto N

Nat Protoc 15 (12) 3894-3941 [2020-12-00; online 2020-11-02]

Fellows programme Magda Bienko

PubMed DOI Crossref

Distinct pre-initiation steps in human mitochondrial translation

Khawaja A, Itoh Y, Remes C, ..., Amunts A, Rorbach J

Nat Commun 11 (1) - [2020-12-00; online 2020-06-10]

Alexey Amunts Fellows programme

PubMed DOI Crossref

Calmodulin acts as a state-dependent switch to control a cardiac potassium channel opening.

Kang PW, Westerlund AM, Shi J, ..., Delemotte L, Cui J

Sci Adv 6 (50) - [2020-12-00; online 2020-12-11]

Fellows programme Lucie Delemotte

PubMed DOI Crossref

Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi

Itoh Y, Naschberger A, Mortezaei N, Herrmann JM, Amunts A

Nat Commun 11 (1) - [2020-12-00; online 2020-10-14]

Alexey Amunts Fellows programme

PubMed DOI Crossref

Universal Single-Residue Terminal Labels for Fluorescent Live Cell Imaging of Microproteins.

Lafranchi L, Schlesinger D, Kimler KJ, Elsässer SJ

Journal of the American Chemical Society 142 (47) 20080-20087 [2020-11-25; online 2020-11-11]

Fellows programme Simon Elsässer

PubMed DOI Crossref

Improved computational analysis of ribosome dynamics from 5′P degradome data using fivepseq

Nersisyan L, Ropat M, Pelechano V

NAR Genomics and Bioinformatics 2 (4) - [2020-11-24; online 2020-11-24]

Fellows programme Vicent Pelechano

PubMed DOI Crossref

Low Shear Stress Increases Recombinant Protein Production and High Shear Stress Increases Apoptosis in Human Cells.

Zhan C, Bidkhori G, Schwarz H, ..., Rockberg J, Chotteau V

iScience 23 (11) 101653 [2020-11-20; online 2020-10-07]

Adil Mardinoglu Fellows programme

PubMed DOI Crossref

Comparative dietary sulfated metabolome analysis reveals unknown metabolic interactions of the gut microbiome and the human host.

Correia MSP, Jain A, Alotaibi W, ..., Rodriguez-Mateos A, Globisch D

Free Radic. Biol. Med. 160 (-) 745-754 [2020-11-20; online 2020-09-11]

Daniel Globisch Fellows programme

PubMed DOI Crossref

Amino Acid Modified RNA Bases as Building Blocks of an Early Earth RNA-Peptide World.

Nainytė M, Müller F, Ganazzoli G, ..., Globisch D, Carell T

Chemistry 26 (65) 14856-14860 [2020-11-20; online 2020-10-14]

Daniel Globisch Fellows programme

PubMed DOI Crossref

Lipoprotein Particles Interact with Membranes and Transfer Their Cargo without Receptors

Plochberger B, Sych T, Weber F, ..., Stangl H, Sezgin E

Biochemistry 59 (45) 4421-4428 [2020-11-17; online 2020-11-04]

Erdinc Sezgin Fellows programme

PubMed DOI Crossref

Redesigning Solvatochromic Probe Laurdan for Imaging Lipid Order Selectively in Cell Plasma Membranes.

Danylchuk DI, Sezgin E, Chabert P, Klymchenko AS

Anal. Chem. 92 (21) 14798-14805 [2020-11-03; online 2020-10-12]

Erdinc Sezgin Fellows programme

PubMed DOI Crossref

Tracking the motion of the KV 1.2 voltage sensor reveals the molecular perturbations caused by a de novo mutation in a case of epilepsy.

Pantazis A, Kaneko M, Angelini M, ..., Saitta SC, Olcese R

J. Physiol. (Lond.) 598 (22) 5245-5269 [2020-11-00; online 2020-09-21]

Fellows programme Lucie Delemotte

PubMed DOI Crossref

Quantification of aromatase binding in the female human brain using [11 C]cetrozole positron emission tomography.

Jonasson M, Nordeman P, Eriksson J, ..., Lubberink M, Comasco E

J Neurosci Res 98 (11) 2208-2218 [2020-11-00; online 2020-08-06]

Erika Comasco Fellows programme

PubMed DOI Crossref

Perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) induce epigenetic alterations and promote human breast cell carcinogenesis in vitro.

Pierozan P, Cattani D, Karlsson O

Arch. Toxicol. 94 (11) 3893-3906 [2020-11-00; online 2020-07-22]

Fellows programme Oskar Karlsson

PubMed DOI Crossref

Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome

Ehrenbolger K, Jespersen N, Sharma H, ..., Vossbrinck CR, Barandun J

PLoS Biol. 18 (10) e3000958 [2020-10-30; online 2020-10-30]

Fellows programme Jonas Barandun

PubMed DOI Crossref

Potential Anticancer Effect of Carvacrol Codrugs on Human Glioblastoma Cells.

Yazici A, Marinelli L, Cacciatore I, ..., Mardinoğlu A, Türkez H

Curr Drug Deliv 18 (3) 350-356 [2020-10-29; online 2020-10-29]

Adil Mardinoglu Fellows programme

PubMed DOI Crossref

Fluidity and Lipid Composition of Membranes of Peroxisomes, Mitochondria and the ER From Oleic Acid-Induced Saccharomyces cerevisiae

Reglinski K, Steinfort-Effelsberg L, Sezgin E, ..., Eggeling C, Erdmann R

Front Cell Dev Biol 8 (-) 574363 [2020-10-29; online 2020-10-29]

Erdinc Sezgin Fellows programme

PubMed DOI Crossref

Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.

Tarbier M, Mackowiak SD, Frade J, ..., Gallant CJ, Friedländer MR

Nat Commun 11 (1) 5445 [2020-10-28; online 2020-10-28]

Fellows programme Magda Bienko Marc Friedländer

PubMed DOI Crossref

Hippocampal neural stem cells are more susceptible to the neurotoxin BMAA than primary neurons: effects on apoptosis, cellular differentiation, neurite outgrowth, and DNA methylation.

Pierozan P, Cattani D, Karlsson O

Cell Death Dis 11 (10) 910 [2020-10-24; online 2020-10-24]

Fellows programme Oskar Karlsson

PubMed DOI Crossref

Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.

Flygaard RK, Mühleip A, Tobiasson V, Amunts A

Nat Commun 11 (1) 5342 [2020-10-22; online 2020-10-22]

Alexey Amunts Fellows programme

PubMed DOI Crossref

Rapid Preparation of a Large Sulfated Metabolite Library for Structure Validation in Human Samples.

Correia MSP, Lin W, Aria AJ, Jain A, Globisch D

Metabolites 10 (10) 415 [2020-10-16; online 2020-10-16]

Daniel Globisch Fellows programme

PubMed DOI Crossref

Network analysis reveals how lipids and other cofactors influence membrane protein allostery.

Westerlund AM, Fleetwood O, Pérez-Conesa S, Delemotte L

J Chem Phys 153 (14) 141103 [2020-10-14; online 2020-10-23]

Fellows programme Lucie Delemotte

PubMed DOI Crossref

The Next Generation of Pattern Recognition Receptor Agonists: Improving Response Rates in Cancer Immunotherapy

O’ Donovan DH, Mao Y, Mele DA

Current medicinal chemistry 27 (34) 5654-5674 [2020-10-11; online 2020-10-11]

Fellows programme Yumeng Mao

PubMed DOI Crossref

TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes.

Wang J, Li B, Marques S, ..., Wei W, Pelechano V

Nucleic Acids Res. 48 (18) e104 [2020-10-09; online 2020-08-21]

Fellows programme Vicent Pelechano

PubMed DOI Crossref

An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility.

Navarro C, Lyu J, Katsori AM, Caridha R, Elsässer SJ

Nat Commun 11 (1) 5095 [2020-10-09; online 2020-10-09]

Fellows programme Simon Elsässer

PubMed DOI Crossref

Receptor occupancy of dual glucagon-like peptide 1/glucagon receptor agonist SAR425899 in individuals with type 2 diabetes.

Eriksson O, Haack T, Hijazi Y, ..., Wagner M, Tillner J

Sci Rep 10 (1) 16758 [2020-10-07; online 2020-10-07]

Fellows programme Olof Eriksson

PubMed DOI Crossref

HEARTBREAK Controls Post-translational Modification of INDEHISCENT to Regulate Fruit Morphology in Capsella.

Dong Y, Majda M, Šimura J, ..., Smith RS, Østergaard L

Curr. Biol. 30 (19) 3880-3888.e5 [2020-10-05; online 2020-08-13]

Fellows programme Tanja Slotte

PubMed DOI Crossref

Progesterone - Friend or foe?

Sundström-Poromaa I, Comasco E, Sumner R, Luders E

Front Neuroendocrinol 59 (-) 100856 [2020-10-00; online 2020-07-28]

Erika Comasco Fellows programme

PubMed DOI Crossref

Male swarming aggregation pheromones increase female attraction and mating success among multiple African malaria vector mosquito species.

Mozūraitis R, Hajkazemian M, Zawada JW, ..., Borg-Karlson AK, Emami SN

Nat Ecol Evol 4 (10) 1395-1401 [2020-10-00; online 2020-08-03]

Fellows programme Marc Friedländer

PubMed DOI Crossref

GPSeq reveals the radial organization of chromatin in the cell nucleus.

Girelli G, Custodio J, Kallas T, ..., Crosetto N, Bienko M

Nat. Biotechnol. 38 (10) 1184-1193 [2020-10-00; online 2020-05-25]

Fellows programme Magda Bienko

PubMed DOI Crossref

Body composition after allogeneic haematopoietic cell transplantation/total body irradiation in children and young people: a restricted systematic review.

Lorenc A, Hamilton-Shield J, Perry R, Stevens M, CTYA HSCT Adipose and Muscle Late Effects Working Group

J Cancer Surviv 14 (5) 624-642 [2020-10-00; online 2020-07-18]

Adil Mardinoglu Fellows programme

PubMed DOI Crossref

Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts.

Mondav R, Bertilsson S, Buck M, ..., Lindström ES, Garcia SL

mSystems 5 (5) - [2020-09-29; online 2020-09-29]

Fellows programme Sarahi Garcia

PubMed DOI Crossref

Discovery of Proteolysis-Targeting Chimera Molecules that Selectively Degrade the IRAK3 Pseudokinase.

Degorce SL, Tavana O, Banks E, ..., Yang B, Edmondson SD

J Med Chem 63 (18) 10460-10473 [2020-09-24; online 2020-09-14]

Fellows programme Yumeng Mao

PubMed DOI Crossref

Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning.

Mohammadi E, Benfeitas R, Turkez H, ..., Uhlen M, Mardinoglu A

Cancers (Basel) 12 (9) - [2020-09-21; online 2020-09-21]

Adil Mardinoglu Fellows programme

PubMed DOI Crossref

Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.

Vaga S, Lee S, Ji B, ..., Engstrand L, Shoaie S

Sci Rep 10 (1) 14977 [2020-09-11; online 2020-09-11]

Fellows programme Saeed Shoaie

PubMed DOI Crossref

Disease, Drugs and Dysbiosis: Understanding Microbial Signatures in Metabolic Disease and Medical Interventions.

Proffitt C, Bidkhori G, Moyes D, Shoaie S

Microorganisms 8 (9) 1381 [2020-09-09; online 2020-09-09]

Fellows programme Saeed Shoaie

PubMed DOI Crossref

Integration of molecular profiles in a longitudinal wellness profiling cohort.

Tebani A, Gummesson A, Zhong W, ..., Uhlen M, Fagerberg L

Nat Commun 11 (1) 4487 [2020-09-08; online 2020-09-08]

Adil Mardinoglu Fellows programme

PubMed DOI Crossref

The RNA exosome shapes the expression of key protein-coding genes.

Wu M, Karadoulama E, Lloret-Llinares M, ..., Jensen TH, Sandelin A

Nucleic Acids Res. 48 (15) 8509-8528 [2020-09-04; online 2020-07-28]

Fellows programme Vicent Pelechano

PubMed DOI Crossref

Systems Biology: A Multi-Omics Integration Approach to Metabolism and the Microbiome.

Son JW, Shoaie S, Lee S

Endocrinol Metab (Seoul) 35 (3) 507-514 [2020-09-00; online 2020-09-22]

Fellows programme Saeed Shoaie

PubMed DOI Crossref

PhenoChip: A single-cell phenomic platform for high-throughput photophysiological analyses of microalgae.

Behrendt L, Salek MM, Trampe EL, ..., Kühl M, Stocker R

Sci Adv 6 (36) eabb2754 [2020-09-00; online 2020-09-02]

Fellows programme Lars Behrendt

PubMed DOI Crossref

Perspectives from Ten Years of Protist Studies by High-Throughput Metabarcoding.

Santoferrara L, Burki F, Filker S, ..., Dunthorn M, McManus GB

J. Eukaryot. Microbiol. 67 (5) 612-622 [2020-09-00; online 2020-07-02]

Fabien Burki Fellows programme

PubMed DOI Crossref

Structural basis of mitochondrial translation.

Aibara S, Singh V, Modelska A, Amunts A

Elife 9 (-) - [2020-08-19; online 2020-08-19]

Alexey Amunts Fellows programme

PubMed DOI Crossref

Unexpected Acetylation of Endogenous Aliphatic Amines by Arylamine N-Acetyltransferase NAT2.

Conway LP, Rendo V, Correia MSP, ..., Sjöblom T, Globisch D

Angew. Chem. Int. Ed. Engl. 59 (34) 14342-14346 [2020-08-17; online 2020-07-08]

Daniel Globisch Fellows programme

PubMed DOI Crossref

Drug Repositioning for P-Glycoprotein Mediated Co-Expression Networks in Colorectal Cancer.

Beklen H, Gulfidan G, Arga KY, Mardinoglu A, Turanli B

Front Oncol 10 (-) 1273 [2020-08-13; online 2020-08-13]

Adil Mardinoglu Fellows programme

PubMed DOI Crossref

Transcriptional mutagenesis dramatically alters genome-wide p53 transactivation landscape.

Liang S, Ezerskyte M, Wang J, Pelechano V, Dreij K

Sci Rep 10 (1) 13513 [2020-08-11; online 2020-08-11]

Fellows programme Vicent Pelechano

PubMed DOI Crossref

Human RTEL1 associates with Poldip3 to facilitate responses to replication stress and R-loop resolution.

Björkman A, Johansen SL, Lin L, ..., Bartek J, Schou KB

Genes Dev. 34 (15-16) 1065-1074 [2020-08-01; online 2020-06-19]

Fellows programme Simon Elsässer

PubMed DOI Crossref

The cyanobacterial neurotoxin β-N-methylamino-L-alanine (BMAA) targets the olfactory bulb region.

Pierozan P, Piras E, Brittebo E, Karlsson O

Arch. Toxicol. 94 (8) 2799-2808 [2020-08-00; online 2020-05-20]

Fellows programme Oskar Karlsson

PubMed DOI Crossref

Predatory colponemids are the sister group to all other alveolates.

Tikhonenkov DV, Strassert JFH, Janouškovec J, ..., Burki F, Keeling PJ

Mol. Phylogenet. Evol. 149 (-) 106839 [2020-08-00; online 2020-04-21]

Fabien Burki Fellows programme

PubMed DOI Crossref

Neuroprotective effects of boron nitride nanoparticles in the experimental Parkinson's disease model against MPP+ induced apoptosis.

Küçükdoğru R, Türkez H, Arslan ME, ..., Cacciatore I, Di Stefano A

Metab Brain Dis 35 (6) 947-957 [2020-08-00; online 2020-03-25]

Adil Mardinoglu Fellows programme

PubMed DOI Crossref

Interference with pancreatic sympathetic signaling halts the onset of diabetes in mice.

Christoffersson G, Ratliff SS, von Herrath MG

Sci Adv 6 (35) eabb2878 [2020-08-00; online 2020-08-26]

Fellows programme Gustaf Christoffersson

PubMed DOI Crossref

Human ovarian cancer intrinsic mechanisms regulate lymphocyte activation in response to immune checkpoint blockade.

Natoli M, Bonito N, Robinson JD, Ghaem-Maghami S, Mao Y

Cancer Immunol. Immunother. 69 (8) 1391-1401 [2020-08-00; online 2020-03-21]

Fellows programme Yumeng Mao

PubMed DOI Crossref

GPCRmd uncovers the dynamics of the 3D-GPCRome.

Rodríguez-Espigares I, Torrens-Fontanals M, Tiemann JKS, ..., Guixà-González R, Selent J

Nat. Methods 17 (8) 777-787 [2020-08-00; online 2020-07-13]

Fellows programme Jens Carlsson

PubMed DOI Crossref

Apparent stiffness of vimentin intermediate filaments in living cells and its relation with other cytoskeletal polymers.

Smoler M, Coceano G, Testa I, Bruno L, Levi V

Biochim Biophys Acta Mol Cell Res 1867 (8) 118726 [2020-08-00; online 2020-04-19]

Fellows programme Ilaria Testa

PubMed DOI Crossref

Automated GMP-Compliant Production of [68Ga]Ga-DO3A-Tuna-2 for PET Microdosing Studies of the Glucagon Receptor in Humans.

Wagner M, Doverfjord JG, Tillner J, ..., Eriksson O, Velikyan I

Pharmaceuticals (Basel, Switzerland) 13 (8) 176 [2020-07-31; online 2020-07-31]

Fellows programme Olof Eriksson

PubMed DOI Crossref

Current Status of COVID-19 Therapies and Drug Repositioning Applications.

Altay O, Mohammadi E, Lam S, ..., Uhlen M, Mardinoglu A

iScience 23 (7) 101303 [2020-07-24; online 2020-06-20]

Adil Mardinoglu Fellows programme

PubMed DOI Crossref

Systems Biology Approaches to Understand the Host-Microbiome Interactions in Neurodegenerative Diseases.

Rosario D, Boren J, Uhlen M, ..., Mardinoglu A, Shoaie S

Front Neurosci 14 (-) 716 [2020-07-08; online 2020-07-08]

Adil Mardinoglu Fellows programme Saeed Shoaie

PubMed DOI Crossref

Pulsed Electric Fields Can Create Pores in the Voltage Sensors of Voltage-Gated Ion Channels.

Rems L, Kasimova MA, Testa I, Delemotte L

Biophys. J. 119 (1) 190-205 [2020-07-07; online 2020-06-08]

Fellows programme Ilaria Testa Lucie Delemotte

PubMed DOI Crossref

Rapid Detection of COVID-19 Coronavirus Using a Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) Diagnostic Platform.

Yu L, Wu S, Hao X, ..., Chen WH, Yin X

Clin. Chem. 66 (7) 975-977 [2020-07-01; online 2020-04-22]

Fellows programme Vicent Pelechano

DOI Crossref

EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotic life

Richter DJ, Berney C, Strassert JFH, Burki F, de Vargas C

- - (-) - [2020-07-01; online 2020-07-01]

Fabien Burki Fellows programme

PubMed DOI Crossref

Quo vadis microRNAs?

Fromm B, Keller A, Yang X, ..., Peterson KJ, Griffiths-Jones S

Trends in Genetics 36 (7) 461-463 [2020-07-00; online 2020-04-16]

Fellows programme Marc Friedländer

PubMed DOI Crossref

Influenza A viruses use multivalent sialic acid clusters for cell binding and receptor activation.

Sieben C, Sezgin E, Eggeling C, Manley S

PLoS Pathog 16 (7) e1008656 [2020-07-00; online 2020-07-08]

Erdinc Sezgin Fellows programme

PubMed DOI Crossref

DNA surface exploration and operator bypassing during target search.

Marklund E, van Oosten B, Mao G, ..., Elf J, Deindl S

Nature 583 (7818) 858-861 [2020-07-00; online 2020-06-24]

Daniel Globisch Fellows programme Sebastian Deindl

PubMed DOI Crossref

A systems biology approach for studying neurodegenerative diseases.

Lam S, Bayraktar A, Zhang C, ..., Uhlen M, Mardinoglu A

Drug Discov. Today 25 (7) 1146-1159 [2020-07-00; online 2020-05-19]

Adil Mardinoglu Fellows programme Saeed Shoaie

PubMed DOI Crossref

Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women.

Chapman MA, Arif M, Emanuelsson EB, ..., Mardinoglu A, Sundberg CJ

Cell Reports 31 (12) 107808 [2020-06-23; online 2020-06-25]

Adil Mardinoglu Fellows programme

PubMed DOI Crossref

Site-Specific Incorporation of Two ncAAs for Two-Color Bioorthogonal Labeling and Crosslinking of Proteins on Live Mammalian Cells.

Meineke B, Heimgärtner J, Eirich J, Landreh M, Elsässer SJ

Cell Reports 31 (12) 107811 [2020-06-23; online 2020-06-25]

Fellows programme Simon Elsässer

PubMed DOI Crossref

Successful delivery of large-size CRISPR/Cas9 vectors in hard-to-transfect human cells using small plasmids.

Søndergaard JN, Geng K, Sommerauer C, ..., Yin X, Kutter C

Commun Biol 3 (1) 319 [2020-06-19; online 2020-06-19]

Claudia Kutter Fellows programme

PubMed DOI Crossref

Adipose tissue morphology, imaging and metabolomics predicting cardiometabolic risk and family history of type 2 diabetes in non-obese men.

Rawshani A, Eliasson B, Rawshani A, ..., Rosengren A, Smith U

Sci Rep 10 (1) 9973 [2020-06-19; online 2020-06-19]

Adil Mardinoglu Fellows programme

PubMed DOI Crossref

Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation.

Tobiasson V, Amunts A

Elife 9 (-) e59264 [2020-06-18; online 2020-06-18]

Alexey Amunts Fellows programme

DOI Crossref

Chaining with Overlaps Revisited

Sahlin K, Mäkinen V

31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020) 161 (-) 25:1--25:12 [2020-06-09; online 2020-06-09]

Fellows programme Kristoffer Sahlin

PubMed DOI Crossref

Sensitive mass spectrometric analysis of carbonyl metabolites in human urine and fecal samples using chemoselective modification.

Lin W, Conway LP, Block A, ..., Löhr JM, Globisch D

Analyst 145 (11) 3822-3831 [2020-06-07; online 2020-05-12]

Daniel Globisch Fellows programme

PubMed DOI Crossref

Plasma membranes are asymmetric in lipid unsaturation, packing and protein shape.

Lorent JH, Levental KR, Ganesan L, ..., Lyman E, Levental I

Nat. Chem. Biol. 16 (6) 644-652 [2020-06-00; online 2020-05-04]

Erdinc Sezgin Fellows programme

PubMed DOI Crossref

Improvement in the Current Therapies for Hepatocellular Carcinoma Using a Systems Medicine Approach.

Ozcan M, Altay O, Lam S, ..., Boren J, Mardinoglu A

Adv Biosyst 4 (6) e2000030 [2020-06-00; online 2020-04-08]

Adil Mardinoglu Fellows programme

PubMed DOI Crossref

Germ-free and microbiota-associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes.

Hausmann A, Russo G, Grossmann J, ..., Sellin ME, Hardt WD

Cell. Microbiol. 22 (6) e13191 [2020-06-00; online 2020-03-04]

Fellows programme Mikael Sellin

PubMed DOI Crossref

Dose and time effects of solar-simulated ultraviolet radiation on the in vivo human skin transcriptome.

Bustamante M, Hernandez-Ferrer C, Tewari A, ..., Nieuwenhuijsen M, Young AR

Br. J. Dermatol. 182 (6) 1458-1468 [2020-06-00; online 2019-11-27]

Fellows programme Marc Friedländer

PubMed DOI Crossref

Intrinsic Dissolution Rate Profiling of Poorly Water-Soluble Compounds in Biorelevant Dissolution Media.

Teleki A, Nylander O, Bergström CAS

Pharmaceutics 12 (6) 493 [2020-05-28; online 2020-05-28]

Alexandra Teleki Fellows programme

PubMed DOI Crossref

Shift in ecological strategy helps marginal populations of shepherd's purse (Capsella bursa-pastoris) to overcome a high genetic load.

Orsucci M, Milesi P, Hansen J, ..., Glémin S, Lascoux M

Proc. Biol. Sci. 287 (1927) 20200463 [2020-05-27; online 2020-05-20]

Fellows programme Pascal Milesi

PubMed DOI Crossref

Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis.

Thomas QA, Ard R, Liu J, ..., Pelechano V, Marquardt S

Nat Commun 11 (1) 2589 [2020-05-22; online 2020-05-22]

Fellows programme Vicent Pelechano

PubMed DOI Crossref

Integrating the "Immunome" in the Stratification of Myelodysplastic Syndromes and Future Clinical Trial Design.

Winter S, Shoaie S, Kordasti S, Platzbecker U

J Clin Oncol 38 (15) 1723-1735 [2020-05-20; online 2020-02-14]

Fellows programme Saeed Shoaie

PubMed DOI Crossref

z-STED Imaging and Spectroscopy to Investigate Nanoscale Membrane Structure and Dynamics.

Barbotin A, Urbančič I, Galiani S, ..., Booth M, Sezgin E

Biophys. J. 118 (10) 2448-2457 [2020-05-19; online 2020-04-16]

Erdinc Sezgin Fellows programme

PubMed DOI Crossref

Histidyl-Proline Diketopiperazine Isomers as Multipotent Anti-Alzheimer Drug Candidates.

Turkez H, Cacciatore I, Arslan ME, ..., Di Stefano A, Mardinoglu A

Biomolecules 10 (5) 737 [2020-05-09; online 2020-05-09]

Adil Mardinoglu Fellows programme

PubMed DOI Crossref

Predicting resolution and image quality in RESOLFT and other point scanning microscopes [Invited].

Bodén A, Casas Moreno X, Cooper BK, York AG, Testa I

Biomed Opt Express 11 (5) 2313-2327 [2020-05-01; online 2020-04-02]

Fellows programme Ilaria Testa

PubMed DOI Crossref

Differential Expression of Immune Genes between Two Closely Related Beetle Species with Different Immunocompetence following Attack by Asecodes parviclava.

Yang X, Fors L, Slotte T, ..., Wheat CW, Hambäck PA

Genome Biol Evol 12 (5) 522-534 [2020-05-01; online 2020-04-14]

Fellows programme Tanja Slotte

PubMed DOI Crossref

Salmonella Typhimurium discreet-invasion of the murine gut absorptive epithelium.

Fattinger SA, Böck D, Di Martino ML, ..., Hardt WD, Sellin ME

PLoS Pathog 16 (5) e1008503 [2020-05-00; online 2020-05-04]

Fellows programme Mikael Sellin

PubMed DOI Crossref

Intestinal epithelial NAIP/NLRC4 restricts systemic dissemination of the adapted pathogen Salmonella Typhimurium due to site-specific bacterial PAMP expression.

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Mucosal Immunol 13 (3) 530-544 [2020-05-00; online 2020-01-17]

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Adil Mardinoglu Fellows programme

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ACS pharmacology & translational science 3 (2) 361-370 [2020-04-10; online 2020-03-31]

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Adil Mardinoglu Fellows programme

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Nat Commun 11 (1) 1666 [2020-04-03; online 2020-04-03]

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J. Comput. Biol. 27 (4) 472-484 [2020-04-00; online 2020-03-16]

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Checknita D, Bendre M, Ekström TJ, ..., Hodgins S, Nilsson KW

Behav. Brain Res. 382 (-) 112476 [2020-03-16; online 2020-01-10]

Erika Comasco Fellows programme

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An atlas of the protein-coding genes in the human, pig, and mouse brain.

Sjöstedt E, Zhong W, Fagerberg L, ..., Uhlén M, Mulder J

Science (New York, N.Y.) 367 (6482) eaay5947 [2020-03-06; online 2020-03-07]

Adil Mardinoglu Fellows programme

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Nat Plants 6 (3) 321-327 [2020-03-00; online 2020-03-02]

Alexey Amunts Fellows programme

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PLoS Comput Biol 16 (3) e1007680 [2020-03-00; online 2020-03-13]

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Lieven C, Beber ME, Olivier BG, ..., Zakhartsev M, Zhang C

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Jamy M, Foster R, Barbera P, ..., Bass D, Burki F

Mol Ecol Resour 20 (2) 429-443 [2020-03-00; online 2019-11-29]

Fabien Burki Fellows programme

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Behrendt L, Trampe EL, Nord NB, ..., Hershey OS, Barton H

Environ. Microbiol. 22 (3) 952-963 [2020-03-00; online 2019-09-09]

Fellows programme Lars Behrendt

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Nat Plants 6 (3) 314-320 [2020-03-00; online 2020-03-09]

Alexey Amunts Fellows programme

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J Phys Chem B 124 (8) 1487-1494 [2020-02-27; online 2020-02-18]

Erdinc Sezgin Fellows programme

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A comprehensive analysis of coding and non-coding transcriptomic changes in cutaneous squamous cell carcinoma.

Das Mahapatra K, Pasquali L, Søndergaard JN, ..., Kristensen LS, Pivarcsi A

Sci Rep 10 (1) 3637 [2020-02-27; online 2020-02-27]

Claudia Kutter Fellows programme

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Energy Landscapes Reveal Agonist Control of G Protein-Coupled Receptor Activation via Microswitches.

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Biochemistry 59 (7) 880-891 [2020-02-25; online 2020-02-07]

Fellows programme Jens Carlsson Lucie Delemotte

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Creating Supported Plasma Membrane Bilayers Using Acoustic Pressure.

Sezgin E, Carugo D, Levental I, Stride E, Eggeling C

Membranes (Basel) 10 (2) 30 [2020-02-18; online 2020-02-18]

Erdinc Sezgin Fellows programme

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Biophysical Characterization of Epigallocatechin-3-Gallate Effect on the Cardiac Sodium Channel Nav1.5.

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Molecules 25 (4) 902 [2020-02-18; online 2020-02-18]

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Front Genet 11 (-) 33 [2020-02-12; online 2020-02-12]

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Regulation of lipid saturation without sensing membrane fluidity.

Ballweg S, Sezgin E, Doktorova M, ..., Hummer G, Ernst R

Nat Commun 11 (1) 756 [2020-02-06; online 2020-02-06]

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Molecular Insights from Conformational Ensembles via Machine Learning.

Fleetwood O, Kasimova MA, Westerlund AM, Delemotte L

Biophys. J. 118 (3) 765-780 [2020-02-04; online 2019-12-21]

Fellows programme Lucie Delemotte

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Abundance and diversity of resistomes differ between healthy human oral cavities and gut.

Carr VR, Witherden EA, Lee S, ..., Gomez-Cabrero D, Moyes DL

Nat Commun 11 (1) 693 [2020-02-04; online 2020-02-04]

Fellows programme Saeed Shoaie

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Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API.

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Bioinformatics 36 (3) 698-703 [2020-02-01; online 2019-09-11]

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The molecular basis for sugar import in malaria parasites.

Qureshi AA, Suades A, Matsuoka R, ..., Delemotte L, Drew D

Nature 578 (7794) 321-325 [2020-02-00; online 2020-01-29]

Fellows programme Lucie Delemotte

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Handling ties in continuous outcomes for confounder adjustment with rank-ordered logit and its application to ordinal outcomes.

Ning Y, Tan CS, Maraki A, ..., Reilly M, Støer NC

Stat Methods Med Res 29 (2) 437-454 [2020-02-00; online 2019-04-03]

Erika Comasco Fellows programme

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Environmental impacts and limitations of third‐generation biobutanol: Life cycle assessment of n ‐butanol produced by genetically engineered cyanobacteria

Nilsson A, Shabestary K, Brandão M, Hudson EP

Journal of Industrial Ecology 24 (1) 205-216 [2020-02-00; online 2019-04-00]

Fellows programme Paul Hudson

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Classification of clear cell renal cell carcinoma based on PKM alternative splicing.

Li X, Turanli B, Juszczak K, ..., Zhang C, Mardinoglu A

Heliyon 6 (2) e03440 [2020-02-00; online 2020-02-19]

Adil Mardinoglu Fellows programme

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Boosting Natural Killer Cell-Mediated Targeting of Sarcoma Through DNAM-1 and NKG2D.

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Front Immunol 11 (-) 40 [2020-01-28; online 2020-01-28]

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Population Genomics of Transitions to Selfing in Brassicaceae Model Systems.

Mattila TM, Laenen B, Slotte T

Methods in molecular biology (Clifton, N.J.) 2090 (-) 269-287 [2020-01-25; online 2020-01-25]

Fellows programme Tanja Slotte

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Docking Finds GPCR Ligands in Dark Chemical Matter.

Ballante F, Rudling A, Zeifman A, ..., Loza MI, Carlsson J

J Med Chem 63 (2) 613-620 [2020-01-23; online 2020-01-13]

Fellows programme Jens Carlsson

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Novel anti-Alzheimer phenol-lipoyl hybrids: Synthesis, physico-chemical characterization, and biological evaluation.

Pagoni A, Marinelli L, Di Stefano A, ..., Vassiliou S, Cacciatore I

Eur J Med Chem 186 (-) 111880 [2020-01-15; online 2019-11-12]

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A set of monomeric near-infrared fluorescent proteins for multicolor imaging across scales.

Matlashov ME, Shcherbakova DM, Alvelid J, ..., Testa I, Verkhusha VV

Nat Commun 11 (1) 239 [2020-01-13; online 2020-01-13]

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Stable stimulated emission depletion imaging of extended sample regions

Alvelid J, Testa I

J. Phys. D: Appl. Phys. 53 (2) 024001 [2020-01-09; online 2019-10-25]

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MirGeneDB 2.0: the metazoan microRNA complement.

Fromm B, Domanska D, Høye E, ..., Friedländer MR, Peterson KJ

Nucleic Acids Res. 48 (D1) D1172 [2020-01-08; online 2019-10-24]

Fellows programme Marc Friedländer

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The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe.

Martínez-Sancho E, Slámová L, Morganti S, ..., Westin J, Fonti P

Sci Data 7 (1) 1 [2020-01-02; online 2020-01-02]

Fellows programme Pascal Milesi

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Protein aggregation in bacteria.

Schramm FD, Schroeder K, Jonas K

FEMS Microbiol Rev 44 (1) 54-72 [2020-01-01; online 2019-10-22]

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Advances in GLP-1 receptor targeting radiolabeled agent development and prospective of theranostics.

Velikyan I, Eriksson O

Theranostics 10 (1) 437-461 [2020-01-01; online 2020-01-01]

Fellows programme Olof Eriksson

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The New Tree of Eukaryotes.

Burki F, Roger AJ, Brown MW, Simpson AGB

Trends in Ecology & Evolution 35 (1) 43-55 [2020-01-00; online 2019-10-09]

Fabien Burki Fellows programme

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Ontogenic succession of thermokarst thaw ponds is linked to dissolved organic matter quality and microbial degradation potential

Peura S, Wauthy M, Simone D, ..., Rautio M, Bertilsson S

Limnol. Oceanogr. 65 (S1) - [2020-01-00; online 2020-01-00]

Fellows programme Sari Peura

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Non‐cyanobacterial diazotrophs dominate nitrogen‐fixing communities in permafrost thaw ponds

Fernandez L, Bertilsson S, Peura S

Limnol. Oceanogr. 65 (S1) - [2020-01-00; online 2020-01-00]

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Super-resolution RESOLFT microscopy of lipid bilayers using a fluorophore-switch dyad

Frawley AT, Wycisk V, Xiong Y, ..., Eggeling C, Anderson HL

Chem Sci 11 (33) 8955-8960 [2020-00-00; online 2020-00-00]

Erdinc Sezgin Fellows programme

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Chapter 7. Bridging the Gap Between Atomistic Molecular Dynamics Simulations and Wet-lab Experimental Techniques: Applications to Membrane Proteins

Delemotte L

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Fellows programme Lucie Delemotte

Publications 2020

136 publications