Publications 2019

Dudley LJ, Cabodevilla AG, Makar AN, Sztacho M, Michelberger T, Marsh JA, Houston DR, Martens S, Jiang X, Gammoh N. (2019) Intrinsic lipid binding activity of ATG16L1 supports efficient membrane anchoring and autophagy.EMBO J. 2019 May 2;38(9). PMID: 30936093

Turco E, Witt M, Abert C, Bock-Bierbaum T, Su MY, Trapannone R, Sztacho M, Danieli A , Shi X, Zaffagnini G, Gamper A, Schuschnig M, Fracchiolla D, Bernklau D , Romanov J, Hartl M, Hurley JH, Daumke O, Martens S. (2019)  FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates. Mol Cell. 2019 Apr 18;74(2):330-346.e11. PMID:  30853400

Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo K, Charnagalov A. (2019) Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Mol Biol Rep. 2019 Apr 12. PMID: 30977085

Elgendy M, Cirò M, Hosseini A, Weiszmann J, Mazzarella L, Ferrari E, Cazzoli R, Curigliano G, DeCensi A, Bonanni B, Budillon A, Pelicci PG, Janssens V, Ogris M, Baccarini M, Lanfrancone L, Weckwerth W, Foiani M, Minucci S. (2019) Combination of Hypoglycemia and Metformin Impairs Tumor Metabolic Plasticity and Growth by Modulating the PP2A-GSK3β-MCL-1 Axis.Cancer Cell. 2019 Apr 10. PMID: 31031016

Nandakumar R, Tschismarov R, Meissner F, Prabakaran T, Krissanaprasit A, Farahani E, Zhang BC, Assil S, Martin A, Bertrams W, Holm CK, Ablasser A, Klause T, Thomsen MK, Schmeck B, Howard KA, Henry T, Gothelf KV, Decker T, Paludan SR. (2019) Intracellular bacteria engage a STING-TBK1-MVB12b pathway to enable paracrine cGAS-STING signalling.Nat Microbiol. 2019 Apr;4(4):701-713. PMID: 30804548

Kriegenburg F, Bas L, Gao J, Ungermann C, Kraft C. (2019) The multi-functional SNARE protein Ykt6 in autophagosomal fusion processes.Cell Cycle. 2019 Mar - Apr;18(6-7):639-651. PMID: 30836834

Dorard C, Cseh B, Ehrenreiter K, Wimmer R, Varga A, Hirschmugl T, Maier B, Kramer K, Fürlinger S, Doma E, Baccarini M. (2019)  RAF dimers control vascular permeability and cytoskeletal rearrangements at endothelial cell-cell junctions. FEBS J. 2019 Mar 3 PMID: 30828992

Schrempf D, Minh BQ, von Haeseler A, Kosio C. (2019) Polymorphism-aware species trees with advanced mutation models, bootstrap and rate heterogeneity. Mol Biol Evol. 2019 Mar 2. PMID: 30825307

Hafner A, Kolbe U, Freund I, Castiglia V, Kovarik P, Poth T, Herster F, Weigand MA, Weber ANR, Dalpke AH, Eigenbrod T. (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. 2019 Feb 21;10:198. PMID: 30846984

Schenk S, Bannister SC, Sedlazeck FJ, Anrather D, Minh BQ, Bileck A, Hartl M, von Haeseler A, Gerner C, Raible F, Tessmar-Raible K. (2019) Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase. Elife. 2019 Feb 15;8 PMID: 30767890

Krunic M, Venhuizen P, Müllauer L, Kaserer B, von Haeseler A. (2019) VARIFI-Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data. J Pers Med. 2019 Feb 1;9(1) PMID: 30717290

Jain A, Perisa D, Fliedner F, von Haeseler A, Ebersberger I. (2019) The Evolutionary Traceability of a Protein. Genome Biol Evol. 2019 Feb 1;11(2):531-545. PMID: 30649284

Osmanagic-Myers, Selma; Kiss, Attila; Manakanatas, Christina; Hamza, Ouafa; Sedlmayer, Franziska; Szabo, Petra L; Fischer, Irmgard; Fichtinger, Petra; Podesser, Bruno K; Eriksson, Maria; Foisner, Roland (2019)  Endothelial progerin expression causes cardiovascular pathology through an impaired mechanoresponse. J CLIN INVEST PMID: 30422822

Tang T, Zhang Y, Wang Y, Cai Z, Lu Z, Li L, Huang R, Hagelkruys A, Matthias P, Zhang H, Seiser C, Xie Y. (2019) HDAC1 and HDAC2 Regulate Intermediate Progenitor Positioning to Safeguard Neocortical Development.Neuron. 2019 Mar 20;101(6):1117-1133 PMID: 30709655

Kollmann S, Grundschober E, Maurer B, Warsch W, Grausenburger R, Edlinger L, Huuhtanen J, Lagger S, Hennighausen L, Valent P, Decker T, Strobl B, Mueller M, Mustjoki S, Hoelbl-Kovacic A, Sexl V. (2019) Twins with different personalities: STAT5B-but not STAT5A-has a key role in BCR/ABL-induced leukemia.Leukemia. 2019 Jan 24. PMID: 30679796

Vunjak M, Versteeg GA. (2019) TRIM proteins. Curr Biol. 2019 Jan 21;29(2):R42-R44. PMID: 30668943

Abert C, Martens S. (2019) Studies of Receptor-Atg8 Interactions During Selective Autophagy.Methods Mol Biol. 2019;1880:189-196. PMID: 30610697

Publications 2018

Beyer, Reinhard; Jandric, Zeljkica; Zutz, Christoph; Gregori, Christa; Willinger, Birgit; Jacobsen, Ilse D; Kovarik, Pavel; Strauss, Joseph; Schüller, Christoph (2018)  Competition of Candida glabrata against Lactobacillus is Hog1 dependent. CELL MICROBIOL:e12943. PMID: 30112857

Tripathy, Ratna; Leca, Ines; van Dijk, Tessa; Weiss, Janneke; van Bon, Bregje W; Sergaki, Maria Christina; Gstrein, Thomas; Breuss, Martin; Tian, Guoling; Bahi-Buisson, Nadia; Paciorkowski, Alexander R; Pagnamenta, Alistair T; Wenninger-Weinzierl, Andrea; Martinez-Reza, Maria Fernanda; Landler, Lukas; Lise, Stefano; Taylor, Jenny C; Terrone, Gaetano; Vitiello, Giuseppina; Del Giudice, Ennio; Brunetti-Pierri, Nicola; D'Amico, Alessandra; Reymond, Alexandre; Voisin, Norine; Bernstein, Jonathan A; Farrelly, Ellyn; Kini, Usha; Leonard, Thomas A; Valence, Stéphanie; Burglen, Lydie; Armstrong, Linlea; Hiatt, Susan M; Cooper, Gregory M; Aldinger, Kimberly A; Dobyns, William B; Mirzaa, Ghayda; Pierson, Tyler Mark; Baas, Frank; Chelly, Jamel; Cowan, Nicholas J; Keays, David Anthony (2018)  Mutations in MAST1 Cause Mega-Corpus-Callosum Syndrome with Cerebellar Hypoplasia and Cortical Malformations. NEURON. PMID: 30449657

Parrini, Matthias; Meissl, Katrin; Ola, Mojoyinola Joanna; Lederer, Therese; Puga, Ana; Wienerroither, Sebastian; Kovarik, Pavel; Decker, Thomas; Müller, Mathias; Strobl, Birgit (2018)  The C-Terminal Transactivation Domain of STAT1 Has a Gene-Specific Role in Transactivation and Cofactor Recruitment. Frontiers in immunology;9:2879. PMID: 30574148

Martens, Sascha (2018)  A division of labor in mTORC1 signaling and autophagy. Sci Signal;11(559). PMID: 30514809

Szappanos, Daniel; Tschismarov, Roland; Perlot, Thomas; Westermayer, Sandra; Fischer, Katrin ; Platanitis, Ekaterini ; Kallinger, Fabian; Novatchkova, Maria; Lassnig, Caroline; Müller, Mathias; Sexl, Veronika; Bennett, Keiryn L; Foong-Sobis, Michelle; Penninger, Josef M; Decker, Thomas (2018)  The RNA helicase DDX3X is an essential mediator of innate antimicrobial immunity. PLOS PATHOG;14(11):e1007397. 2018 Nov 26 PMID: 30475900

Platanitis, Ekaterini ; Decker, Thomas (2018) ). Regulatory Networks Involving STATs, IRFs, and NFB in Inflammation. Frontiers in immunology;9:2542, 2018 Nov 13 PMID:  30483250

Yuan, Jimin; Ng, Wan Hwa; Tian, Zizi; Yap, Jiajun; Baccarini, Manuela; Chen, Zhongzhou; Hu, Jiancheng (2018)  Activating mutations in MEK1 enhance homodimerization and promote tumorigenesis. Sci Signal;11(554), 2018 Oct 13 PMID: 30377225

Danieli, Alberto ; Martens, Sascha (2018)  p62-mediated phase separation at the intersection of the ubiquitin-proteasome system and autophagy. J CELL SCI;131(19).PMID: 30287680

Bas L; Papinski, Daniel; Kraft, Claudine (2018)  Ykt6 mediates autophagosome-vacuole fusion. Molecular & cellular oncology.5(6):e1526006.PMID: 30525099

Pfanzagl, Vera; Nys, Kevin; Bellei, Marzia; Michlits, Hanna; Mlynek, Georg; Battistuzzi, Gianantonio; Djinovic-Carugo, Kristina; Van Doorslaer, Sabine; Furtmüller, Paul G; Hofbauer, Stefan; Obinger, Christian (2018)  Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage. J BIOL CHEM;293(38):14823-14838. 2018 Sep 21 PMID: 30072383

Kraft, Claudine; Boya, Patricia; Codogno, Patrice; Elazar, Zvulun; Eskelinen, Eeva-Liisa; Farrés, Judith; Kirkin, Vladimir; Jungbluth, Heinz; Martinez, Ana; Pless, Ole; Primard, Charlotte; Proikas-Cezanne, Tassula; Simonsen, Anne; Reggiori, Fulvio (2018)  Driving next-generation autophagy researchers towards translation (DRIVE), an international PhD training program on autophagy. AUTOPHAGY:1-5. PMID: 30176150

Gómez-Sánchez, Rubén; Rose, Jaqueline; Guimarães, Rodrigo; Mari, Muriel; Papinski, Daniel; Rieter, Ester; Geerts, Willie J; Hardenberg, Ralph; Kraft, Claudine; Ungermann, Christian; Reggiori, Fulvio (2018)  Atg9 establishes Atg2-dependent contact sites between the endoplasmic reticulum and phagophores. J CELL BIOL;217(8):2743-2763. PMID: 29848619

Nguyen, Lam-Tung; von Haeseler, Arndt; Minh, Bui Quang (2018). Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site plus Gamma Model. SYST BIOL;67(3):552-558. PMID: 29186593

Bas L, Papinski D, Licheva M, Torggler R, Rohringer S, Schuschnig M, Kraft C. (2018) Reconstitution reveals Ykt6 as the autophagosomal SNARE in autophagosome-vacuole fusion. J Cell Biol. 2018 Aug 10 PMID: 30097514

Yuan, Jimin; Ng, Wan Hwa; Lam, Paula Y P; Wang, Yu; Xia, Hongping; Yap, Jiajun; Guan, Shou Ping; Lee, Ann S G; Wang, Mei; Baccarini, Manuela; Hu, Jiancheng (2018)  The dimer-dependent catalytic activity of RAF family kinases is revealed through characterizing their oncogenic mutants. ONCOGENE 2018 Jun 21 PMID: 29930381

Hoang, Diep Thi; Chernomor, Olga; von Haeseler, Arndt; Minh, Bui Quang; Le, Sy Vinh (2018). UFBoot2: Improving the Ultrafast Bootstrap Approximation. MOL BIOL EVOL;35(2):518-522. PMID: 29077904

Lando, David; Basu, Srinjan; Stevens, Tim J; Riddell, Andy; Wohlfahrt, Kai J; Cao, Yang; Boucher, Wayne; Leeb, Martin; Atkinson, Liam P; Lee, Steven F; Hendrich, Brian; Klenerman, Dave; Laue, Ernest D (2018)  Combining fluorescence imaging with Hi-C to study 3D genome architecture of the same single cell. NAT PROTOC;13(5):1034-1061. PMID: 29674753

Zaffagnini, Gabriele; Savova, Adriana; Danieli, Alberto; Romanov, Julia; Tremel, Shirley; Ebner, Michael; Peterbauer, Thomas; Sztacho, Martin; Trapannone, Riccardo; Tarafder, Abul K; Sachse, Carsten; Martens, Sascha (2018). p62 filaments capture and present ubiquitinated cargos for autophagy. EMBO J. PMID: 29343546

Orbán-Németh, Zsuzsanna; Beveridge, Rebecca; Hollenstein, David M; Rampler, Evelyn; Stranzl, Thomas; Hudecz, Otto; Doblmann, Johannes; Schlögelhofer, Peter; Mechtler, Karl (2018). Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data. NAT PROTOC;13(3):478-494. PMID: 29419816

Fracchiolla, Dorotea; Martens, Sascha (2018). Sorting out "non-canonical" autophagy. EMBO J. PMID: 29431607

Benke, Stefan; Agerer, Benedikt; Haas, Lisa; Stöger, Martin; Lercher, Alexander; Gabler, Lisa; Kiss, Izabella; Scinicariello, Sara; Berger, Walter; Bergthaler, Andreas; Obenauf, Anna C and Versteeg, Gijs A. (2018). Human tripartite motif protein 52 is required for cell context-dependent proliferation Oncotarget;17(9):13565-13581. PMID: 29568378

Lučić, Iva; Rathinaswamy, Manoj K; Truebestein, Linda; Hamelin, David J; Burke, John E; Leonard, Thomas A (2018). Conformational sampling of membranes by Akt controls its activation and inactivation. P NATL ACAD SCI USA. PMID: 29632185

Alves, Ricardo J Eloy; Minh, Bui Quang; Urich, Tim; von Haeseler, Arndt; Schleper, Christa (2018). Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. NAT COMMUN;9(1):1517. PMID: 29666365

Hoang, Diep Thi; Vinh, Le Sy; Flouri, Tomá?; Stamatakis, Alexandros; von Haeseler, Arndt; Minh, Bui Quang (2018). MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC EVOL BIOL;18(1):11. PMID: 29390973

Uhse, Simon; Pflug, Florian G; Stirnberg, Alexandra; Ehrlinger, Klaus; von Haeseler, Arndt; Djamei, Armin (2018). In vivo insertion pool sequencing identifies virulence factors in a complex fungal-host interaction. PLOS BIOLOGY;16(4):e2005129. PMID: 29684023

Muhar, Matthias; Ebert, Anja; Neumann, Tobias; Umkehrer, Christian; Jude, Julian; Wieshofer, Corinna; Rescheneder, Philipp; Lipp, Jesse J; Herzog, Veronika A; Reichholf, Brian; Cisneros, David A; Hoffmann, Thomas; Schlapansky, Moritz F; Bhat, Pooja; von Haeseler, Arndt; Köcher, Thomas; Obenauf, Anna C; Popow, Johannes; Ameres, Stefan L; Zuber, Johannes (2018). SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. SCIENCE. PMID: 29622725

Pflug, Florian G; von Haeseler, Arndt (2018). TRUmiCount: Correctly counting absolute numbers of molecules using unique molecular identifiers. BIOINFORMATICS. PMID: 29672674

Müller, Christoph; Krunic, Milica; Wendt, Judith; von Haeseler, Arndt; Okamoto, Ichiro (2018). Germline Variants in the POT1-Gene in High-Risk Melanoma Patients in Austria. G3-Genes Genomes Genetics. PMID: 29523635

Baumgartner, Christian; Toifl, Stefanie; Farlik, Matthias; Halbritter, Florian; Scheicher, Ruth; Fischer, Irmgard; Sexl, Veronika; Bock, Christoph; Baccarini, Manuela (2018). An ERK-Dependent Feedback Mechanism Prevents Hematopoietic Stem Cell Exhaustion. Cell stem cell.;22(6):879-892.e6. PMID: 29804890

Sedlyarov, Vitaly; Eichner, Ruth; Girardi, Enrico; Essletzbichler, Patrick; Goldmann, Ulrich; Nunes-Hasler, Paula; Srndic, Ismet; Moskovskich, Anna; Heinz, Leonhard X; Kartnig, Felix; Bigenzahn, Johannes W; Rebsamen, Manuele; Kovarik, Pavel; Demaurex, Nicolas; Superti-Furga, Giulio (2018). The Bicarbonate Transporter SLC4A7 Plays a Key Role in Macrophage Phagosome Acidification. Cell Host Microbe;23(6):766-774.e5. PMID: 29779931

Porpaczy, Edit; Tripolt, Sabrina; Hoelbl-Kovacic, Andrea; Gisslinger, Bettina; Bago-Horvath, Zsuzsanna; Casanova-Hevia, Emilio; Clappier, Emmanuelle; Decker, Thomas; Fajmann, Sabine; Fux, Daniela A; Greiner, Georg; Gueltekin, Sinan; Heller, Gerwin; Herkner, Harald; Hoermann, Gregor; Kiladjian, Jean-Jacques; Kolbe, Thomas; Kornauth, Christoph; Krauth, Maria-Theresa; Kralovics, Robert; Muellauer, Leonhard; Mueller, Mathias; Prchal-Murphy, Michaela; Putz, Eva Maria; Raffoux, Emmanuel; Schiefer, Ana-Iris; Schmetterer, Klaus; Schneckenleithner, Christine; Simonitsch-Klupp, Ingrid; Skrabs, Cathrin; Sperr, Wolfgang R; Staber, Philipp Bernhard; Strobl, Birgit; Valent, Peter; Jaeger, Ulrich; Gisslinger, Heinz; Sexl, Veronika (2018). Aggressive B-cell lymphomas in patients with myelofibrosis receiving JAK1/2 inhibitor therapy. BLOOD. PMID: 29907599

Zaffagnini, Gabriele; Savova, Adriana; Danieli, Alberto; Romanov, Julia; Tremel, Shirley; Ebner, Michael; Peterbauer, Thomas; Sztacho, Martin; Trapannone, Riccardo; Tarafder, Abul K; Sachse, Carsten; Martens, Sascha (2018). Phasing out the bad-How SQSTM1/p62 sequesters ubiquitinated proteins for degradation by autophagy. AUTOPHAGY. PMID: 29929426

Vidak, Sandra; Georgiou, Konstantina; Fichtinger, Petra; Naetar, Nana; Dechat, Thomas; Foisner, Roland (2018)  Nucleoplasmic lamins define growth-regulating functions of lamina-associated polypeptide 2α in progeria cells. J CELL SCI. PMID: 29361532

Nicolussi, Andrea; Dunn, Joe Dan; Mlynek, Georg; Bellei, Marzia; Zamocky, Marcel; Battistuzzi, Gianantonio; Djinovic-Carugo, Kristina; Furtmüller, Paul G; Soldati, Thierry; Obinger, Christian (2018) Secreted heme peroxidase from Dictyostelium discoideum: Insights into catalysis, structure, and biological role.J BIOL CHEM;293(4):1330-1345. PMID: 29242189

Leonard, Thomas A (2018). Reply to Agarwal: Activity against nuclear substrates is not necessarily mediated by nuclear Akt. P NATL ACAD SCI USA. PMID: 29907610

Publications 2017

Kovarik, Pavel; Ebner, Florian; Sedlyarov, Vitaly (2017). Posttranscriptional regulation of cytokine expression. Cytokine.;89:21-26. PMID: 26586165

Prakash, C. and A. von Haeseler (2017). An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Non-uniformity of the Expected Fragment Starting Point and Coverage Profile. J COMPUT BIOL;24(3):200-212. PMID: 27661099

Fracchiolla, D.; Zens,B.; S. Martens (2017). In Vitro Reconstitution of Atg8 Conjugation and Deconjugation. METHOD ENZYMOL;587:377–390. PMID: 28253967

Thanisch, Katharina; Song, Congdi; Engelkamp, Dieter; Koch, Jeannette; Wang, Audrey; Hallberg, Einar; Foisner, Roland; Leonhardt, Heinrich; Stewart, Colin L; Joffe, Boris; Solovei, Irina (2017). Nuclear envelope localization of LEMD2 is developmentally dynamic and lamin A/C dependent yet insufficient for heterochromatin tethering. DIFFERENTIATION;94:58-70. PMID: 28056360

Andrea Majoros, Ekaterina Platanitis, Elisabeth Kernbauer-Hölz, Felix Rosebrock, Mathias Müller and Thomas Decker (2017). Canonical and noncanonical aspects of JAK-STAT signaling: lessons from interferons for cytokine responses Frontiers in immunology;8(29). PMID: 28184222

Michael Ebner, Iva Lučić, Thomas A. Leonard, and Ivan Yudushkin (2017). PI(3,4,5)P3 Engagement Restricts Akt Activity to Cellular Membranes MOL CELL;65(3):416-431. PMID: 28157504