Computation Research Unit of IIT@SEMM
Research & Applications portal
* These authors contributed equally to the work.
Ceol A, Muller H,
The MI Bundle: Enabling Network and Structural Biology in genome visualization tools.
Bioinformatics, 2015, 10.1093/bioinformatics/btv431
Mosca R, Tenorio-Laranga J, Olivella R, Alcalde V, Ceol A, Soler-López M, Aloy P,
dSysMap: Exploring the edgetic role of disease mutations.
Nature Methods, 2015, 10.1038/nmeth.328
Masseroli M, Pinoli P, Venco F, Kaitoua A, Jalili V, Palluzzi F, Muller H, Ceri S
GenoMetric Query Language: A novel approach to large-scale genomic data management.
Angione C*, Costanza J*, Carapezza P, Lió P, Nicosia P
Analysis and design of molecular machines.
Theoretical Computer Science, 2015, ISSN 0304-39710.1016/j.tcs.2015.01.030
Costanza J, Zammataro L, Nicosia G
Programming Living Machines: the case study of Escherichia coli. (Book chapter)
Biomimetic and Biohybrid Systems, Third International Conference, Living Machines 2014, Milan, Italy, July 30 – August 1, 2014. Proceedings, Lecture Notes in Computer Science Volume 8608, 2014, pp 377-37910.1007/978-3-319-09435-9_35
Sabo A, ..., Muller H, Guccione E, Campaner S, Amati B
Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis.
Nature 511.7510 (2014): 488-492. 10.1038/nature13537
Muller H, Marzi MJ, Nicassio F
IsomiRage: From Functional Classification to Differential Expression of miRNA Isoforms.
Frontiers in bioengineering and biotechnology 2 (2014)10.3389/fbioe.2014.00038
Blasche S, Arens S, Ceol A., Siszler G, Schmidt MA, Häuser R, Schwarz F, Wuchty S, Aloy P, Uetz P, Stradal T, Kögl M
The EHEC-host interactome reveals novel targets for the translocated intimin receptor
Scientific Reports 4,Article number: 753110.1038/srep07531
Venco F*, Vaskin Y* , Ceol A., Muller H.
SMITH: A LIMS for handling next-generation sequencing workflows
BMC Bioinformatics (accepted), 2014
Hauser R, Ceol A, Rajagopala SV, Mosca R, Siszler G, Wermke N, Sikorski P, Schwarz F, Schick M, Wuchty S, Aloy P, Uetz P
A Second-generation Protein-Protein Interaction Network of Helicobacter pylori.
Molecular & Cellular Proteomics (2014) 10.1186/1471-2105-15-S1-S8
Zammataro L., De Molfetta R., Bucci G., Ceol A., Muller H.
AnnotateGenomicRegions: A web application.
BMC Bioinformatics 15.1 (2014): 1-7., DOI: 10.1186/1471-2105-15-S1-S8
Mosca R.*, Ceol A.*, Stein A., Olivella R., Aloy P.
3did: a catalogue of domain-based interactions of known three-dimensional structure.
Nucleic Acids Res., 2013. DOI: 10.1093/nar/gkt887
Mosca R.*, Pons T.*, Ceol A.*, Valencia A., Aloy P.
Towards a detailed atlas of protein-protein interactions.
Current Opinion in Structural Biology, 2013. DOI:10.1016/
Ficara F., Crisafulli L., Lin C., Iwasaki M., Smith K. S., Zammataro L., Cleary M. L.
Pbx1 restrains myeloid maturation while preserving lymphoid potential in hematopoietic progenitors.
Journal of cell science, 2013. DOI:10.1242/jcs.125435
Dellino G. I., Cittaro D., Piccioni R., Luzi L., Banfi S., Segalla S., Cesaroni M. et al.
Genome-wide mapping of human DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing.
Genome research, 23(1), 1-11. DOI:10.1101/gr.142331.112
Fragola G., Germain P.-L., Laise P., Cuomo A., Blasimme A., Gross F., Signaroldi E., Bucci G. et al.
Cell reprogramming requires silencing of a core subset of polycomb targets.
PLoS genetics, 9(2), e1003292. DOI:10.1371/journal.pgen.1003292
Giovarelli M., Bucci G., Pasero M., Gherzi R., Briata P.
KSRP silencing favors neural differentiation of P19 teratocarcinoma cells.
Biochimica et biophysica acta, 1829(5), 469-479. DOI:10.1016/j.bbagrm.2013.02.008
Marzi M. J., Puggioni E. M. R., Dall Olio V., Bucci G., Bernard L., Bianchi F., Crescenzi M. et al.
Differentiation-associated microRNAs antagonize the Rb-E2F pathway to restrict proliferation.
The Journal of cell biology, 199(1), 77-95. DOI:10.1083/jcb.201206033
Pasero M., Giovarelli M., Bucci G., Gherzi R., Briata P.
Bone morphogenetic protein/SMAD signaling orients cell fate decision by impairing KSRP-dependent microRNA maturation.
Cell reports, 2(5), 1159-68. DOI:10.1016/j.celrep.2012.10.020
Fumagalli M., Rossiello F., Clerici M., Barozzi S., Cittaro D., Kaplunov J. M., Bucci G. et al.
Telomeric DNA damage is irreparable and causes persistent DNA-damage-response activation.
Nature cell biology, 14(4), 355-65. DOI:10.1038/ncb2466
Perna D., Faga G., Verrecchia A., Gorski M., ..., Muller H., Amati B.
Genome-wide mapping of Myc binding and gene regulation in serum-stimulated fibroblasts.
Oncogene, 31(13), 1695-709. DOI:10.1038/onc.2011.359
Mariani L., Chiroli E., Nezi L., Muller H., Piatti S., Musacchio A., Ciliberto A.
Role of the Mad2 dimerization interface in the spindle assembly checkpoint independent of kinetochores.
Current biology : CB, 22(20), 1900-8. DOI:10.1016/j.cub.2012.08.028