network systems,biological data integration

Development of computational tools for candidate tumor gene prioritization

Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis
Arianna Sabo`, Theresia R. Kress,Mattia Pelizzola1, Stefano de Pretis, Marcin Gorski, Alessandra Tesi, Marco J.Morelli, Pranami Bora, Mirko Doni, Alessandro Verrecchia, Claudia Tonelli, Giovanni Faga`, Valerio Bianchi, Alberto Ronchi, Diana Low, Heiko Muller, Ernesto Guccione, Stefano Campaner & Bruno Amati
Nature 2014, 511, 488..
Doi:10.1038/nature13537

AnnotateGenomicRegions: A web application.
Zammataro L., De Molfetta R., Bucci G., Ceol A., Muller H.
BMC Bioinformatics 15.1 (2014): 1-7.
DOI: 10.1186/1471-2105-15-S1-S8

Genome-wide mapping of Myc binding and gene regulation in serum-stimulated fibroblasts
Perna D., Faga G., Verrecchia A., Gorski M., ..., Muller H., Amati B..
Oncogene, 31(13), 1695-709.
DOI:10.1038/onc.2011.359

Role of the Mad2 dimerization interface in the spindle assembly checkpoint independent of kinetochores.
Mariani L., Chiroli E., Nezi L., Muller H., Piatti S., Musacchio A., Ciliberto A.
Current biology : CB, 22(20), 1900-8.
DOI:10.1016/j.cub.2012.08.028

Identification and analysis of co-occurrence networks with NetCutter
Heiko Muller and Francesco Mancuso
Plos One, 2008, Vol. 3 (9), e3178
DOI: 10.1371/journal.pone.0003178

Localizing hotspots of antisense transcription
Giacomo Finocchiaro, Maria Stella Carro, Stephanie Francois, Paola Parise,
Valentina DiNinni and Heiko Muller
Nucleic Acids Research, 2007, Vol. 35 (5), 1488–1500
Doi:10.1093/nar/gkm027

Graph-based identification of cancer signaling pathways from published gene expression signatures using PubLiME
Giacomo Finocchiaro, Francesco Mattia Mancuso, Davide Cittaro and Heiko Muller
Nucleic Acids Research, 2007, Vol. 35 (7), 2343–2355
Doi:10.1093/nar/gkm119

GenePicker: replicate analysis of Affymetrix gene expression microarrays
Finocchiaro G., Parise P., Minardi S. P., Alcalay M., Muller H.
Bioinformatics, 2004, Vol. 20 (18), 3670-3672
Doi: 10.1093/bioinformatics/bth416

APAF1 is a transcriptional target for E2F and p53
M. Cristina Moroni, Emma S. Hickman, Eros Lazzerini Denchi, Greta Caprara, Elena Colli, Francesco Cecconi, Heiko Müller & Kristian Helin
Nature Cell Biology 2001 Jun;3(6):552-8
Doi:10.1038/35078527

E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis.
Muller H, Bracken AP, Vernell R, Moroni MC, Christians F, Grassilli E, Prosperini E, Vigo E, Oliner JD, Helin K.
Genes Dev. 2001 Feb 1;15(3):267-85.
Doi: 10.1101/gad.864201

Induction of S-phase entry by E2F transcription factors depends on their nuclear localization.
Muller H, Moroni MC, Vigo E, Petersen BO, Bartek J, Helin K
Mol Cell Biol 1997 Sep;17(9):5508-5520

Cyclin D1 expression is regulated by the retinoblastoma protein.
Muller H, Lukas J, Schneider A, Warthoe P, Bartek J, Eilers M, Strauss M
Proc Natl Acad Sci U S A 1994 Apr 12;91(8):2945-2949
doi: 10.1073/pnas.91.8.2945

Identification of differentially expressed mRNA species by an improved display technique (DDRT-PCR).
Bauer D, Muller H, Reich J, Riedel H, Ahrenkiel V, Warthoe P, Strauss M
Nucleic Acids Res 1993 Sep 11;21(18):4272-4280
doi: 10.1093/nar/21.18.4272