Publications 2020

146 publications

Ulipristal Acetate for Treatment of Premenstrual Dysphoric Disorder: A Proof-of-Concept Randomized Controlled Trial
Comasco E, Kopp Kallner H, Bixo M, ..., Epperson CN, Sundström-Poromaa I
AJP - (-) appi.ajp.2020.2 [2020-12-10; online 2020-12-10]
Erika Comasco
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
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
Pooled CRISPRi screening of the cyanobacterium Synechocystis sp PCC 6803 for enhanced industrial phenotypes
Yao L, Shabestary K, Björk SM, ..., Jahn M, Hudson EP
Nat Commun 11 (1) - [2020-12-00; online 2020-04-03]
Paul Hudson
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
JAK inhibition reduces SARS-CoV-2 liver infectivity and modulates inflammatory responses to reduce morbidity and mortality.
Stebbing J, Sánchez Nievas G, Falcone M, ..., Abizanda P, Lauschke VM
Sci Adv - (-) - [2020-11-13; online 2020-11-13]
Claudia Kutter
The effect of Toll-like receptor stimulation on the motility of regulatory T cells.
Chodaczek G, Pagni PP, Christoffersson G, ..., Wegrzyn AS, von Herrath M
J. Autoimmun. - (-) 102563 [2020-11-12; online 2020-11-12]
Gustaf Christoffersson
A genomic catalog of Earth’s microbiomes
Nayfach S, None , Roux S, ..., Kyrpides NC, Eloe-Fadrosh EA
Nat Biotechnol - (-) - [2020-11-09; online 2020-11-09]
Sarahi Garcia
Lipoprotein Particles Interact with Membranes and Transfer Their Cargo without Receptors
Plochberger B, Sych T, Weber F, ..., Stangl H, Sezgin E
Biochemistry - (-) - [2020-11-04; online 2020-11-04]
Erdinc Sezgin
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
Genome-wide detection of DNA double-strand breaks by in-suspension BLISS.
Bouwman BAM, Agostini F, Garnerone S, ..., Roukos V, Crosetto N
Nat Protoc - (-) - [2020-11-02; online 2020-11-02]
Magda Bienko
Rpb4 and Puf3 imprint and post-transcriptionally control the stability of a common set of mRNAs in yeast.
Garrido-Godino AI, Gupta I, Gutiérrez-Santiago F, ..., Pelechano V, Navarro F
RNA Biol - (-) 1-15 [2020-11-01; online 2020-11-01]
Vicent Pelechano
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]
Jonas Barandun
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]
Magda Bienko Marc Friedländer
Potential Anticancer Effect of Carvacrol Codrugs on Human Glioblastoma Cells.
Yazici A, Marinelli L, Cacciatore I, ..., Mardinoğlu A, Türkez H
Curr Drug Deliv - (-) - [2020-10-27; online 2020-10-27]
Adil Mardinoglu
Neuroimaging the menstrual cycle: A multimodal systematic review.
Dubol M, Epperson CN, Sacher J, ..., Sundström-Poromaa I, Comasco E
Front Neuroendocrinol 60 (-) 100878 [2020-10-22; online 2020-10-22]
Erika Comasco
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]
Lucie Delemotte
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]
Vicent Pelechano
Character and environmental lability of cyanobacteria‐derived dissolved organic matter
Patriarca C, Sedano‐Núñez VT, Garcia SL, ..., Tranvik LJ, Hawkes JA
Limnol. Oceanogr. - (-) - [2020-10-09; online 2020-10-09]
Sarahi Garcia
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
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
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]
Magda Bienko
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]
Sarahi Garcia
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]
Yumeng Mao
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
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
Anticancer effects of novel NSAIDs derivatives on cultured human glioblastoma cells.
Özdemir Ö, Marinelli L, Cacciatore I, ..., Mardinoglu A, Turkez H
Z Naturforsch C J Biosci - (-) - [2020-09-04; online 2020-09-04]
Adil Mardinoglu
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]
Vicent Pelechano
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
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) - [2020-09-00; online 2020-09-02]
Lars Behrendt
A molecular timescale for the origin of red algal-derived plastids
Strassert JFH, Irisarri I, Williams TA, Burki F
- - (-) - [2020-08-21; online 2020-08-21]
Fabien Burki
Structural basis of mitochondrial translation
Aibara S, Singh V, Modelska A, Amunts A
Elife 9 (-) - [2020-08-19; online 2020-08-19]
Alexey Amunts
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
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
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]
Vicent Pelechano
Phylogenomic Insights into the Origin of Primary Plastids
Irisarri I, Strassert JFH, Burki F
- - (-) - [2020-08-04; online 2020-08-04]
Fabien Burki
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]
Simon Elsässer
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]
Jens Carlsson
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 2020-08-00]
Fabien Burki
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 [2020-07-30; online 2020-06-24]
Daniel Globisch Sebastian Deindl
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
Model membrane systems to reconstitute immune cell signaling.
Céspedes PF, Beckers D, Dustin ML, Sezgin E
FEBS J. - (-) - [2020-07-18; online 2020-07-18]
Erdinc Sezgin
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
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]
Marc Friedländer
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 Saeed Shoaie
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
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]
Marc Friedländer
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
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
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
Histidyl-Proline Diketopiperazine Isomers as Multipotent Anti-Alzheimer Drug Candidates.
Turkez H, Cacciatore I, Arslan ME, ..., Di Stefano A, Mardinoglu A
Biomolecules 10 (5) - [2020-05-09; online 2020-05-09]
Adil Mardinoglu
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]
Ilaria Testa
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]
Mikael Sellin
High photon count rates improve the quality of super-resolution fluorescence fluctuation spectroscopy
Schneider F, Hernandez-Varas P, Christoffer Lagerholm B, ..., Eggeling C, Urbančič I
J. Phys. D: Appl. Phys. 53 (16) 164003 [2020-04-15; online 2020-02-13]
Erdinc Sezgin
Neuroimaging premenstrual dysphoric disorder: A systematic and critical review.
Dubol M, Epperson CN, Lanzenberger R, Sundström-Poromaa I, Comasco E
Front Neuroendocrinol 57 (-) 100838 [2020-04-00; online 2020-04-05]
Erika Comasco
An atlas of human metabolism.
Robinson JL, Kocabaş P, Wang H, ..., Uhlén M, Nielsen J
Sci Signal 13 (624) - [2020-03-24; online 2020-03-24]
Adil Mardinoglu
Addressing the heterogeneity in liver diseases using biological networks.
Lam S, Doran S, Yuksel HH, ..., Uhlen M, Mardinoglu A
Brief. Bioinformatics - (-) - [2020-03-23; online 2020-03-23]
Adil Mardinoglu
Monoamine oxidase A genotype and methylation moderate the association of maltreatment and aggressive behaviour.
Checknita D, Bendre M, Ekström TJ, ..., Hodgins S, Nilsson KW
Behav. Brain Res. 382 (-) 112476 [2020-03-16; online 2020-01-10]
Erika Comasco
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) - [2020-03-06; online 2020-03-07]
Adil Mardinoglu
MEMOTE for standardized genome-scale metabolic model testing.
Lieven C, Beber ME, Olivier BG, ..., Zakhartsev M, Zhang C
Nat. Biotechnol. 38 (3) 272-276 [2020-03-00; online 2020-03-04]
Adil Mardinoglu Saeed Shoaie
Life in the dark: far-red absorbing cyanobacteria extend photic zones deep into terrestrial caves.
Behrendt L, Trampe EL, Nord NB, ..., Hershey OS, Barton H
Environ. Microbiol. 22 (3) 952-963 [2020-03-00; online 2019-09-09]
Lars Behrendt
Structure of a minimal photosystem I from the green alga Dunaliella salina.
Perez-Boerema A, Klaiman D, Caspy I, ..., Amunts A, Nelson N
Nat Plants 6 (3) 321-327 [2020-03-00; online 2020-03-02]
Alexey Amunts
Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly
Chen M, Perez-Boerema A, Zhang L, ..., Li S, Amunts A
Nat Plants 6 (3) 314-320 [2020-03-00; online 2020-03-09]
Alexey Amunts
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
Creating Supported Plasma Membrane Bilayers Using Acoustic Pressure.
Sezgin E, Carugo D, Levental I, Stride E, Eggeling C
Membranes (Basel) 10 (2) - [2020-02-18; online 2020-02-18]
Erdinc Sezgin
Radial Organization in the Mammalian Nucleus.
Crosetto N, Bienko M
Front Genet 11 (-) 33 [2020-02-12; online 2020-02-12]
Magda Bienko
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]
Erdinc Sezgin
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]
Lucie Delemotte
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]
Saeed Shoaie
Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API.
Desvignes T, Loher P, Eilbeck K, ..., Halushka MK, Pantano L
Bioinformatics 36 (3) 698-703 [2020-02-01; online 2019-09-11]
Marc Friedländer
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]
Lucie Delemotte
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
Boosting Natural Killer Cell-Mediated Targeting of Sarcoma Through DNAM-1 and NKG2D.
Sayitoglu EC, Georgoudaki AM, Chrobok M, ..., Sutlu T, Duru AD
Front Immunol 11 (-) 40 [2020-01-28; online 2020-01-28]
Adil Mardinoglu
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 2019-12-17]
Jens Carlsson
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]
Adil Mardinoglu
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]
Ilaria Testa
Three dimensional parallelized RESOLFT nanoscopy for volumetric live cell imaging
Bodén A, Pennacchietti F, Testa I
- - (-) - [2020-01-09; online 2020-01-09]
Ilaria Testa
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]
Marc Friedländer
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]
Pascal Milesi
Protein aggregation in bacteria.
Schramm FD, Schroeder K, Jonas K
FEMS Microbiol Rev 44 (1) 54-72 [2020-01-01; online 2019-10-22]
Kristina Jonas
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 2020-01-00]
Fabien Burki
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