Ruprecht-Karls-Universität Heidelberg
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Publications by HBIGS PhD students:

Publications in 2019

Bageritz J, Willnow P, Valentini E, Leible S, Boutros M, Teleman AA (2019) Gene expression atlas of a developing tissue by single cell expression correlation analysis. Nature Methods, doi:

Buchmuller BC*, Herbst K*, Meurer M, Kirrmaier D, Sass E, Levy ED, Knop M (*equal contribution) (2019) Pooled clone collections by multiplexed CRISPR-Cas12a-assisted gene tagging in yeast. Nat Commun, doi: 10.1038/s41467-019-10816-7

Valls AF, Knipper K, Giannakouri E, Sarachaga V, Hinterkopf S, Wuehrl M, Shen Y, Radhakrishnan P, Klose J, Ulrich A, Schneider M, Augustin HG, Ruiz de Almodovar C, Schmidt T (2019) VEGFR1+ metastasis-associated macrophages contribute to metastatic angiogenesis and influence colorectal cancer patient outcome. Clin Cancer Res, doi: 10.1158/1078-0432.CCR-18-2123

Dederer V, Khmelinskii A, Huhn AG, Okreglak V, Knop M, Lemberg MK (2019) Cooperation of mitochondrial and ER factors in quality control of tail-anchored proteins. Elife, doi: 10.7554/eLife.45506

Zindler F, Beedgen F, Braunbeck T (2019) Time-course of coiling activity in zebrafish (Danio rerio) embryos exposed to ethanol as an endpoint for developmental neurotoxicity (DNT) – Hidden potential and underestimated challenges. Chemosphere,

Wagner N, Norlin N, Gierten J, de Medeiros G, Balázs B, Wittbrodt J, Hufnagel L, Prevedel R (2019) Instantaneous isotropic volumetric imaging of fast biological processes. Nat Methods, doi: 10.1038/s41592-019-0393-z.

Sarropoulos I, Marin R, Cardoso-Moreira M, Kaessmann H (2019) Developmental dynamics of lncRNAs across mammalian organs and species. Nature, doi: 10.1038/s41586-019-1341-x

Frank T, Nawroth P, Kuner R (2019) Structure–function relationships in peripheral nerve contributions to diabetic peripheral neuropathy. Pain, doi: 10.1097/j.pain.0000000000001530

Münchau S, Deutsch R, de Castro IJ, Hielscher T, Heber N, Niesler B, Lusic M, Stanifer ML, Boulant S (2019) Hypoxic environment promotes barrier formation in human intestinal epithelial cells through regulation of miRNA-320a expression. Mol Cell Biol, doi: 10.1128/MCB.00553-18

Denninger P, Reichelt A, Schmidt VAF, Mehlhorn DG, Asseck LY, Stanley CE, Keinath NF, Evers JF, Grefen C, Grossmann G (2019) Distinct RopGEFs Successively Drive Polarization and Outgrowth of Root Hairs. Curr Biol, doi: 10.1016/j.cub.2019.04.059

Lytvynenko I, Paternoga H, Thrun A, Balke A, Müller TA, Chiang CH, Nagler K, Tsaprailis G, Anders S, Bischofs I, Maupin-Furlow JA, Spahn CMT, Joazeiro CAP (2019) Alanine Tails Signal Proteolysis in Bacterial Ribosome-Associated Quality Control Cell, 178, 1–15,

Devant JM, Hofhaus G, Bhella D, Hansman GS (2019) Heterologous expression of human norovirus GII.4 VP1 leads to assembly of T=4 virus-like particles. Antiviral Res, doi: 10.1016/j.antiviral.2019.05.010

Upmeier zu Belzen J... Schmelas C ...Eils R (2019) Leveraging implicit knowledge in neural networks for functional dissection and engineering of proteins. Nature Machine Intelligence, 1, 225–235

Ahmed M, Legrand C, Yagüe Relimpio A, Beretta CA, Muschko A, Wegehingel S, Müller HM, Sehr P, Will DW, Lewis JD, Nickel W (2019) A time-resolved live cell imaging assay to identify small molecule inhibitors of FGF2 signaling. FEBS Lett, doi: 10.1002/1873-3468

Tisler S, Zindler F, Freeling F, Nodler K, Toelgyesi L, Braunbeck T, Zwiener C (2019) Transformation Products of Fluoxetine Formed by Photodegradation in Water and Biodegradation in Zebrafish Embryos (Danio rerio). Environ Sci Technol, 53,13, 7400

Wei T, Weiler SME, Tóth M, Sticht C, Lutz T, Thomann S, De La Torre C, Straub B, Merker S, Ruppert T, Marquardt J, Singer S, Gretz N, Schirmacher P, Breuhahn K (2019) YAP-dependent induction of UHMK1 supports nuclear enrichment of the oncogene MYBL2 and proliferation in liver cancer cells. Oncogene, doi: 10.1038/s41388-019-0801-y

Ramakrishna P, Ruiz-Duarte P, Rance GA, Schubert M, Vordermaier V, Vu LD, Murphy E, Vilches-Barro A, Swarup K, Moirangthem K, Jørgensen B, van de Cotte B, Goh T, Lin Z, Voβ U, Beeckman T, Bennett MJ, Gevaert K, Maizel A, De Smet I (2019) EXPANSIN A1-mediated radial swelling of pericycle cells positions anticlinal cell divisions during lateral root initiation. Proc Natl Acad Sci U S A, doi: 10.1073/pnas.1820882116

Kumar D*, Golchoubian B*, Belevich I, Jokitalo E, Schlaitz AL (*equal contribution) (2019) REEP3 and REEP4 determine the tubular morphology of the endoplasmic reticulum during mitosis. Mol Biol Cell, doi: 10.1091/mbc.E18-11-0698

López-Salmerón V, Schürholz AK, Li Z, Schlamp T, Wenzl C, Lohmann JU, Greb T, Wolf S (2019) Inducible, Cell Type-Specific Expression in Arabidopsis thaliana Through LhGR-Mediated Trans-Activation. J Vis Exp, doi: 10.3791/59394

Duman C, Yaqubi K, Hoffmann A, Acikgöz AA, Korshunov A, Bendszus M, Herold-Mende C, Liu HK, Alfonso J (2019) Acyl-CoA-Binding Protein Drives Glioblastoma Tumorigenesis by Sustaining Fatty Acid Oxidation. Cell Metab, doi: 10.1016/j.cmet.2019.04.004

Bettenworth V, Steinfeld B, Duin H, Petersen K, Streit WR, Bischofs I, Becker A (2019) Phenotypic Heterogeneity in Bacterial Quorum Sensing Systems. J Mol Biol, doi: 10.1016/j.jmb.2019.04.036

Mehnert AK*, Simon CS*, Guizetti J (*equal contribution) (2019) Immunofluorescence staining protocol for STED nanoscopy of Plasmodium-infected red blood cells. Mol Biochem Parasitol, doi: 10.1016/j.molbiopara.2019.02.007

Tabatabai J, Fakhiri J, Meyburg J, Linse KP, Xu M, Söderlund-Venermo M, Grimm D, Schnitzler P (2019) Severe Human Bocavirus 1 Respiratory Tract Infection in an Immunodeficient Child With Fatal Outcome. Pediatr Infect Dis J, doi: 10.1097/INF.0000000000002354

Hoffmann MD, Aschenbrenner S, Grosse S, Rapti K, Domenger C, Fakhiri J, Mastel M, Börner K, Eils R, Grimm D, Niopek D (2019) Cell-specific CRISPR-Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins. Nucleic Acids Res, doi: 10.1093/nar/gkz271

Kmietczyk V, Riechert E, Kalinski L, Boileau E, Malovrh E, Malone B, Gorska A, Hofmann C, Varma E, Jürgensen L, Kamuf-Schenk V, Altmüller J, Tappu R, Busch M, Most P, Katus HA, Dieterich C, Völkers M (2019) m6A-mRNA methylation regulates cardiac gene expression and cellular growth. Life Sci Alliance, doi: 10.26508/lsa.201800233

Stöth M, Valls AF, Chen M, Hidding S, Knipper K, Shen Y, Klose J, Ulrich A, Ruiz de Almodovar C, Schneider M, Schmidt T (2019) Splenectomy reduces lung metastases and tumoral and metastatic niche inflammation. Int J Cancer, doi: 10.1002/ijc.32378

Diederichs S, Tonnier V, Marz M, Dreher SI, Geisbusch A, Richter W (2019) Regulation of WNT5A and WNT11 during MSC in vitro chondrogenesis: WNT inhibition lowers BMP and hedgehog activity, and reduces hypertrophy. Cell Mol Life Sci, doi:10.1007/s00018-019-03099-0

Bragado Alonso S, Reinert JK, Marichal N, Massalini S, Berninger B, Kuner T, Calegari F (2019) An increase in neural stem cells and olfactory bulb adult neurogenesis improves discrimination of highly similar odorants. EMBO J, 38, 6, e98791, doi: 10.15252/embj.201798791

Sachdeva R, Fleming T, Schumacher D, Homberg S, Stilz K, Mohr F, Wagner AH, Tsvilovskyy V, Mathar I, Freichel M (2019) Methylglyoxal evokes acute Ca2+ transients in distinct cell types and increases agonist-evoked Ca2+ entry in endothelial cells via CRAC channels. Cell Calcium, 78, 66-75

Moraes CB, Witt G ... Pöhner I ... Wade RC ... Gul S (2019) Accelerating Drug Discovery Efforts for Trypanosomatidic Infections Using an Integrated Transnational Academic Drug Discovery Platform. SLAS Discovery, 24, 3, 346-361

Hammouda OT, Böttger F, Wittbrodt J, Thumberger T (2019) Swift Large-scale Examination of Directed Genome Editing. PLoS One, 14, 3, e0213317

López-Salmerón V, Cho H, Tonn N, Greb T (2019) The Phloem as a Mediator of Plant Growth Plasticity. Curr Biol, 29, 5, 173

Lischik CQ, Adelmann L, Wittbrodt J (2019) Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentation. PLoS One, 14, 3, e0212956

Yücel SS, Stelzer W, Lorenzoni A, Wozny M, Langosch D, Lemberg MK (2019) The Metastable XBP1u Transmembrane Domain Defines Determinants for Intramembrane Proteolysis by Signal Peptide Peptidase. Cell Rep, 26, 3087–3099

Schmidt RM, Schessner JP, Borner GH, Schuck S (2019) The proteasome biogenesis regulator Rpn4 cooperates with the unfolded protein response to promote ER stress resistance. Elife, doi: 10.7554/eLife.43244

Hübner JM, Müller T, Papageorgiou DN, Mauermann M, Krijgsveld J, Russell RB, Ellison DW, Pfister SM, Pajtler KW, Kool M (2019) EZHIP / CXorf67 mimics K27M mutated oncohistones and functions as an intrinsic inhibitor of PRC2 function in aggressive posterior fossa ependymoma. Neuro Oncol,

Yang Y, Lenherr E, Gromes R, Wang S, Wirtz M, Hell R, Peskan-Berghöfer T, Scheffzek K, Rausch T (2019) Plant glutathione biosynthesis revisited: Redox-mediated activation of glutamylcysteine ligase does not require homo-dimerization. Biochem J, doi: 10.1042/BCJ20190072

Tsingos E, Höckendorf B, Sütterlin T, Kirchmaier S, Grabe N, Centanin L, Wittbrodt J (2019) Retinal stem cells modulate proliferative parameters to coordinate post-embryonic morphogenesis in the eye of fish. Elife, 8, e42646.

Fakhiri J, Nickl M, Grimm D (2019) Rapid and Simple Screening of CRISPR Guide RNAs (gRNAs) in Cultured Cells Using Adeno-Associated Viral (AAV) Vectors. Methods Mol Biol, 1961, 111-126

Heinrich P, Braunbeck T (2019) Bioavailability of microplastic-bound pollutants in vitro: The role of adsorbate lipophilicity and surfactants. Comp Biochem Physiol C Toxicol Pharmacol, doi: 10.1016/j.cbpc.2019.03.012

Liu Y, Mi Y, Müller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Frank M, Germain PL, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, Bena FS, Zhou H, Dehio C, Testa G, Saez-Rodriguez J, Antonarakis SE, Hardt WD, Aebersold R (2019) Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nat Biotechnol, doi: 10.1038/s41587-019-0037-y

Yan Y, Rato C, Rohland L, Preissler S, Ron D (2019) MANF antagonizes nucleotide exchange by the endoplasmic reticulum chaperone BiP. Nat Commun, 10, 1, 541

Niemeyer J*, Mentrup T*, Heidasch R*, Müller SA, Biswas U, Meyer R, Papadopoulou AA, Dederer V, ..., Lichtenthaler SF, Lemberg MK, Schröder B (*equal contibution) (2019) The intramembrane protease SPPL2c promotes male germ cell development by cleaving phospholamban. EMBO Rep, doi: 10.15252/embr.201846449

Guerra M, Frey D, Hagner M, Dittrich S, Paulsen M, Mall MA, Schultz C (2019) Cathepsin G Activity as a New Marker for Detecting Airway Inflammation by Microscopy and Flow Cytometry. ACS Central Science, DOI: 10.1021/acscentsci.8b00933

Ernst AS*, Böhler LI*, Hagenston AM, Hoffmann A, Heiland S, Sticht C, Bendszus M, Hecker M, Bading H, Marti HH, Korff T, Kunze R (*equal contribution) (2019) EphB2-dependent signaling promotes neuronal excitotoxicity and inflammation in the acute phase of ischemic stroke. Acta Neuropathol Commun, 7, 1, 15

Ivey Williams MP, Rigon M, Straka T, Hörner SJ, Thiel M, Gretz N, Hafner M, Reischl M, Rudolf R (2019) A Novel Optical Tissue Clearing Protocol for Mouse Skeletal Muscle to Visualize Endplates in Their Tissue Context. Front Cell Neurosci,

Hafner A*, Kolbe U*, Freund I, Castiglia V, Kovarik P, Poth T, Herster F, Weigand MA, Weber ANR, Dalpke AH, Eigenbrod T (*equal contribution) (2019) Crucial Role of Nucleic Acid Sensing via Endosomal Toll-Like Receptors for the Defense of Streptococcus pyogenes in vitro and in vivo. Front Immunol, doi: 10.3389/fimmu.2019.00198

Dabiri Y, Gama-Brambila RA, Taškova K, Herold K, Reuter S, Adjaye J, Utikal J, Mrowka R, Wang J, Andrade-Navarro MA, Cheng X (2019) Imidazopyridines as Potent KDM5 Demethylase Inhibitors Promoting Reprogramming Efficiency of Human iPSCs. iScience, doi: 10.1016/j.isci.2019.01.012

Lafarga V, Sung HM, Haneke K, Roessig L, Pauleau AL, Bruer M, Rodriguez-Acebes S, Lopez-Contreras AJ, Gruss OJ, Erhardt S, Mendez J, Fernandez-Capetillo O, Stoecklin G (2019) TIAR marks nuclear G2/M transition granules and restricts CDK1 activity under replication stress. EMBO Rep, 20, 1, e46224

Ruoff K, Kilic T, Devant J, Koromyslova A, Ringel A, Hempelmann A, Geiss C, Graf J, Haas M, Roggenbach I, Hansman G (2019) Structural Basis of Nanobodies Targeting the Prototype Norovirus. J Virol, doi: 10.1128/JVI.02005-18

Tsopoulidis N, Kaw S, Laketa V, Kutscheidt S, Baarlink C, Stolp B, Grosse R, Fackler OT (2019) T cell receptor-triggered nuclear actin network formation drives CD4+ T cell effector functions. Sci Immunol, 4, 31

Monaco S, Baur K, Hellwig A, Hölzl-Wenig G, Mandl C, Ciccolini F (2019) A Flow Cytometry-Based Approach for the Isolation and Characterization of Neural Stem Cell Primary Cilia. Front Cell Neurosci,

Miyashima S, Roszak P, Sevilem I, Toyokura K, Blob B, Heo JO, Mellor N, Help-Rinta-Rahko H, Otero S, Smet W, Boekschoten M, Hooiveld G, Hashimoto K, Smetana O, Siligato R, Wallner ES, Mähönen AP, Kondo Y, Melnyk CW, Greb T, Nakajima K, Sozzani R, Bis (2019) Mobile PEAR transcription factors integrate positional cues to prime cambial growth. Nature, doi: 10.1038/s41586-018-0839-y

Wild K, Juaire KD, Soni K, Shanmuganathan V, Hendricks A, Segnitz B, Beckmann R, Sinning I (2019) Reconstitution of the human SRP system and quantitative and systematic analysis of its ribosome interactions. Nucleic Acids Res, doi: 10.1093/nar/gky1324

Oliveira AM, Litke C, Paldy E, Hagenston AM, Lu J, Kuner R, Bading H, Mauceri D (2019) Epigenetic control of hypersensitivity in chronic inflammatory pain by the de novo DNA methyltransferase Dnmt3a2. Mol Pain, doi: 10.1177/1744806919827469

Dwivedi D, Kumari A, Rathi S, Mylavarapu SVS, Sharma M (2019) The dynein adaptor Hook2 plays essential roles in mitotic progression and cytokinesis. J Cell Biol, doi: 10.1083/jcb.201804183

Rauner M, Baschant U, ... Colucci S, Muckenthaler M,...Altamura S (2019) Transferrin receptor 2 controls bone mass and pathological bone formation via BMP and Wnt signaling. Nature Metabolism, 1, 111

Neves J, Haider T, Gassmann M, Muckenthaler MU (2019) Iron Homeostasis in the Lungs-A Balance between Health and Disease. Pharmaceuticals (Basel), 12, 1

Baser A, Skabkin M, Kleber S, Dang Y, Gülcüler Balta GS, Kalamakis G, Göpferich M, Ibañez DC, Schefzik R, Lopez AS, Bobadilla EL, Schultz C, Fischer B, Martin-Villalba A (2019) Onset of differentiation is post-transcriptionally controlled in adult neural stem cells. Nature, 566, 7742, 100

Müller TG*, Sakin V*, Müller B (2019) A Spotlight on Viruses—Application of Click Chemistry to Visualize Virus-Cell Interactions. Molecules, 24, 3, 481

Fakhiri J, Schneider MA, Puschhof J, Stanifer M, Schildgen V, Holderbach S, Voss Y, El Andari J, Schildgen O, Boulant S, Meister M, Clevers H, Yan Z, Qiu J, Grimm D (2019) Novel Chimeric Gene Therapy Vectors Based on Adeno-Associated Virus and Four Different Mammalian Bocaviruses. Mol Ther Methods Clin Dev, 12, 202-222

Malovrh E, Völkers M (2019) Crosstalk Between the Endoplasmic Reticulum and mTOR Signaling. Circ Res, doi: 10.1161/CIRCRESAHA.118.314326

Breckwoldt MO, Bode J, Sahm F, Krüwel T, Solecki G, Hahn A, Wirthschaft P, Berghoff AS, Haas M, Venkataramani V, von Deimling A, Wick W, Herold-Mende C, Heiland S, Platten M, Bendszus M, Kurz FT, Winkler F, Tews B (2019) Correlated MRI and Ultramicroscopy (MR-UM) of Brain Tumors Reveals Vast Heterogeneity of Tumor Infiltration and Neoangiogenesis in Preclinical Models and Human Disease. Front Neurosci, doi: 10.3389/fnins.2018.01004

Staudacher I, Seehausen S, Gierten J, Illg C, Schweizer PA, Katus HA, Thomas D (2019) Cloning and characterization of zebrafish K2P13.1 (THIK-1) two-pore-domain K+ channels. J Mol Cell Cardiol, doi: 10.1016/j.yjmcc.2018.11.013