Original articles (Papers addressing biological questions)

Benetka W, Koranda M, Maurer-Stroh S, Pittner F, and Eisenhaber F. Farnesylation or geranylgeranylation? Efficient assays for testing protein prenylation in vitro and in vivo. BMC Biochem 7:6, 2006

Bogner-Strauss JG, Prokesch A, Sanchez-Cabo F, Rieder D, Hackl H, Duszka K et al. Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and trageted by PPAR-gamma. Cell Mol Life Sci 67(23):4049-4064, 2010 (6.090)

Boria I, Gruber AR, Tanzer A, Bernhart SH, Lorenz R, Mueller MM et al. Nematode sbRNAs: Homologs of Vertebrate Y RNAs. J Mol Evol 70(4):346-358, 2010 (2.762)

Burkard TR, Rix U, Breitwieser FP, Superti-Furga G, and Colinge J. A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib. PLoS Comput Biol 6(11):e1001001, 2010 (5.759)

Burkard TR, Planyavsky M, Kaupe I, Breitwieser FP, Bürkstürmmer T, Bennett KL et al. Initial characterization of the human central proteome. BMC Systems Biology 5(1):17, 2011 (4.064)

Camus M, Tosolini M, Mlecnik B, Pages F, Kirilovsky A, Berger A et al. Coordination of intratumoral immune reaction and human colorectal cancer recurrence. Cancer Res 69(6):2685-2693, 2009 (7.672)

Camus M, Tosolini M, Mlecnik B, Pages F, Kirilovsky A, Berger A et al. Coordination of intratumoral immune reaction and human colorectal cancer recurrence. Cancer Res 69(6):2685-2693, 2009 (7.672)

ENCODE Project Consortium, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007;447(7146):799-816.

Galon J, Costes A, Sanchez-Cabo F, Kirilovsky A, Mlecnik B, Lagorce-Pages C, Tosolini M, Camus M, Berger A, Wind P, Zinzindohoue F, Bruneval P, Cugnenc PH, Trajanoski Z, Fridman WH, and Pages F. Type, density, and location of immune cells within human colorectal tumors predict clinical outcome. Science 313(5795):1960-1964, 2006

Gruber AR, Koper-Emde D, Marz M, Tafer H, Bernhart S, Obernosterer G, Mosig A, Hofacker IL, Stadler PF, and Benecke BJ. Invertebrate 7SK snRNAs. J Mol Evol, 2008

Hackl H, Burkard TR, Sturn A, Rubio R, Schleiffer A, Tian S, Quackenbush J, Eisenhaber F, and Trajanoski Z. Molecular processes during fat cell development revealed by gene expression profiling and functional annotation. Genome Biol 6(13):R108, 2005

Hanada R, Leibbrandt A, Hanada T, Kitaoka S, Furuyashiki T, Fujihara H et al. Central control of fever and female body temperature by RANKL/RANK. Nature 462(7272):505-509, 2009 (31.434)

Haura EB, Muller A, Breitwieser FP, Li J, Grebien F, Colinge J et al. Using iTRAQ combined with tandem affinity purification to enhance low-abundance proteins associated with somatically mutated EGFR core complexes in lung cancer. J Proteome Res 10(1):182-190, 2011 (5.132)

He Q, Bardet A, Patton B, Purvis J, Johnston J, Paulson A, Gogol M, Stark A, and Zeitlinger J. High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nature Genetics. 43(5):414-420, 2011 (34.284)

Kulterer B, Friedl G, Jandrositz A, Sanchez-Cabo F, Prokesch A, Paar C, Scheideler M, Windhager R, Preisegger K-H, and Trajanoski Z. Gene Expression Profiling of Human Mesenchymal Stem Cells derived from Bone Marrow during Expansion and Osteoblast Differentiation. BMC Genomics 8(1):70, 2007

Kurzbauer R, Teis D, de Araujo ME, Maurer-Stroh S, Eisenhaber F, Bourenkov GP, Bartunik HD, Hekman M, Rapp UR, Huber LA, and Clausen T. Crystal structure of the p14/MP1 scaffolding complex: how a twin couple attaches mitogen-activated protein kinase signaling to late endosomes. Proc Natl Acad Sci USA 101(30):10984-10989, 2004

Lakota K, Thallinger GG, Cucnik S, Bozic B, Mrak-Poljsak K, Ambrozic A et al. Could antibodies against Serum Amyloid A function as physiological regulators in humans? Autoimmunity 44(2):149-158, 2011 (2.813)

Laschober GT, Ruli D, Hofer E, Muck C, Carmona-Gutierrez D, Ring J et al. Identification of evolutionarily conserved genetic regulators of cellular aging. Aging Cell 9(6):1084-1097, 2010 (7.554)

Lorenz C, Gesell T, Zimmermann B, Schoeberl U, Bilusic I, Rajkowitsch L et al. Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts. Nucleic Acids Res 38(11):3794-3808, 2010 (6.878)

Marth K, Novatchkova M, Focke-Tejkl M, Jenisch S, Jager S, Kabelitz D et al. Tracing antigen signatures in the human IgE repertoire. Mol Immunol 47(14):2323-2329, 2010 (3.202)

Mlecnik B, Tosolini M, Charoentong P, Kirilovsky A, Bindea G, Berger A et al. Biomolecular network reconstruction identifies T cell homing factors associated with survival in colorectal cancer. Gastroenterology 138(4):1429-1440, 2010 (12.591)

Mlecnik B, Tosolini M, Kirilovsky A, Berger A, Bindea G, Meatchi T, Bruneval P, Trajanoski Z, Fridman W-H, Pages F, Galon J. Histopathological-based prognostic factors of colorectal cancers are associated with the state of the local immune reaction. J Clin Oncol. 29(6):610-618, 2011 (17.793)

Mlecnik B, Sanchez-Cabo F, Charoentong P, Bindea G, Pages F, Berger A et al. Data integration and exploration for the identification of molecular mechanisms in tumor-immune cells interaction. BMC Genomics 11(Suppl 1):S7, 2010 (3.926)

Müller WG, Rieder D, Karpova TS, John S, Trajanoski Z, and McNally JG. Organization of chromatin and histone modifications at a transcription site. J Cell Biol 177(6):957-967, 2007

Müller WG, Rieder D, Kreth G, Cremer C, Trajanoski Z, and McNally JG. Generic features of tertiary chromatin structure as detected in natural chromosomes. Mol Cell Biol 24(21):9359-9370, 2004

Niault T, Sobcak I, Meissl K, Piazzolla D, Maurer G, Kern F et al. From autoinhibition to inhibition in trans: the Raf-1 regulatory domain inhibits Rok-alpha kinase activity. J Cell Biol 187(3):335-342, 2009 (9.120)

Obermayr E, Sanchez-Cabo F, Tea MK, Singer CF, Krainer M, Fischer MB et al. Assessment of a six gene panel for the molecular detection of circulating tumor cells in the blood of female cancer patients. BMC Cancer 10(1):666, 2010 (2.660)

Pages F, Berger A, Camus F, Sanchez-Cabo F, Costes A, Molidor R, Mlecnik B, Kirilovsky A, Nilsson M, Damotte D, Meatchi T, Bruneval P, Cugnenenc PH, Trajanoski Z, Fridman WH, and Galon J. Effector memory T cells, early metastasis, and survival in colorectal cancer. N Engl J Med 353(25):2654-2666, 2005

Pages F, Kirilovsky A, Mlecnik B, Asslaber M, Tosolini M, Bindea G et al. In situ cytotoxic and memory T cells predict outcome in patients with early-stage colorectal cancer. J Clin Oncol 27(35):5944-5951, 2009 (17.157)

Parson W, Kirchebner R, Mühlmann R, Renner K, Kofler A, Schmidt S, and Kofler R. Cancer cell line identification by short tandem repeat profiling: power and limitations. FASEB J 19(3):434-436, 2005

Pirnia F, Pawlak M, Thallinger GG, Gierke B, Templin MF, Kappeler A et al. Novel functional profiling approach combining reverse phase protein microarrays and human 3-D ex vivo tissue cultures: expression of apoptosis-related proteins in human colon cancer. Proteomics 9(13):3535-3548, 2009 (4.586)

Prokesch A, Bogner-Strauss JG, Hackl H, Rieder D, Neuhold C, Walenta E, Krogsdam A, Scheideler M, Papak C, Wong WC, Vinson C, Eisenhaber F, Trajanoski Z. Arxes: Retrotransposed genes required for adipogenesis Nucl Acids Res. 39(8):3224-3239, 2011 (7.479)

Querol-Audi J, Konecsni T, Pous J, Carugo O, Fita I, Verdaguer N et al. Minor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition. FEBS Lett 583(1):235-240, 2009 (3.263)

Rabitsch KP, Gregan J, Schleiffer A, Javerzat JP, Eisenhaber F, and Nasmyth K. Two fission yeast homologs of Drosophila Mei-S332 are required for chromosome segregation during meiosis I and II. Curr Biol 14(4):287-301, 2004

Schmidt S, Rainer J, Riml S, Ploner C, Jesacher S, Achmuller C, Presul E, Skvortsov S, Crazzolara R, Fiegl M, Raivio T, Janne OA, Geley S, Meister B, and Kofler R. Identification of glucocorticoid-response genes in children with acute lymphoblastic leukemia. Blood 107(5):2061-2069, 2006

Schneider G, Neuberger G, Wildpaner M, Tian S, Berezovsky I, Eisenhaber F. Application of a sensitive collection heuristic for very large protein families: evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases. BMC Bioinformatics 7:164, 2006

Schnorrer F, Schonbauer C, Langer CC, Dietzl G, Novatchkova M, Schernhuber K et al. Systematic genetic analysis of muscle morphogenesis and function in Drosophila. Nature 464(7286):287-291, 2010 (31.434)

Silverman J, Takai H, Buonomo SB, Eisenhaber F, and de Lange T. Human Rif1, ortholog of a yeast telomeric protein, is regulated by ATM and 53BP1 and functions in the S-phase checkpoint. Genes Dev 18(17):2108-2119, 2004

Smit van Dixhoorn MG, Munir R, Sussman G, Stad R, de Haan M, van der Hoeven T, Rauwerda H, Breit TM, Thallinger GG, Wadee AA. Gene expression profiling of suppressor mechanisms in tuberculosis. Mol Immunol. 2008 Mar;45(6):1573-1586.

Tian S. A 20 Residues Motif Delineates the Furin Cleavage Site and its Physical Properties May Influence Viral Fusion. Biochemistry Insights 2:9-20, 2009 (0.000)

Tian S and Jianhua W. Comparative study of the binding pockets of mammalian proprotein convertases and its implications for the design of specific small molecule inhibitors. Int J Biol Sci 6(1):89-95, 2010 (0.000)

Tschernatsch MMO, Mlecnik B, Trajanoski Z, Zechner R, and Zimmermann R. LPL-mediated lipolysis of VLDL induces an upregulation of AU-rich mRNAs and an activation of HuR in endothelial cells. Atherosclerosis, 2006

Visvanathan M, Netzer M, Seger M, Adagarla BS, Baumgartner C, Sittampalam S et al. Oncogenes and pathway identification using filter-based approaches between various carcinoma types in lung. International Journal of Computational Biology and Drug Design 2(3):236-251, 2009 (0.000)

Washietl S and Eisenhaber F. Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses. BMC Bioinformatics 4(1):55, 2003

Washietl S, Hofacker IL, Lukasser M, Hüttenhofer A, and Stadler PF. Genome-wide mapping of conserved RNA Secondary Structures predicts Thousands of functional Non-Coding RNAs in Human. Nat Biotechnol 23(11):1383-1390, 2005

Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermuller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigo R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, and Stadler PF. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res 17(6):852-864, 2007

Watrin E, Schleiffer A, Tanaka K, Eisenhaber F, Nasmyth K, Peters JM. Human Scc4 is required for cohesin binding to chromatin, sister-chromatid cohesion, and mitotic progression. Curr Biology 16(9):863-874, 2006

Weber C, Pickl-Herk A, Khan AG, Strauss S, Carugo O, and Blaas D. Predictive bioinformatic identification of minor receptor group human rhinoviruses. FEBS Lett 583(15):2547-2551, 2009 (3.139)

Will S, Missal K, Hofacker IL, Stadler PF, and Backofen R. Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comp Biol, 2007. PLoS Comput Biol. 2007 Apr 13;3(4):e65. Epub 2007 Feb 22.

Zimmermann B, Gesell T, Chen D, Lorenz C, and Schroeder R. Monitoring Genomic Sequences During SELEX Using High-Throughput Sequencing: Neutral SELEX. PLoS ONE 5(2):e9169, 2010 (0.000)

Zimmermann R, Strauss JG, Haemmerle G, Schoiswohl G, Birner-Gruenberger R, Riederer M, Lass A, Neuberger G, Eisenhaber F, Hermetter A, and Zechner R. Fat mobilization in adipose tissue is promoted by adipose triglyceride lipase. Science 306(5700):1383-1386, 2004