Other Publications
PEER REVIEWED PUBLICATIONS
Oncogene. 2011 Aug 22. doi: 10.1038/onc.2011.359
Genome-wide mapping of Myc binding and gene regulation in serum-stimulated fibroblasts.
Perna D,Fagà G,Verrecchia A,Gorski, MM,Barozzi I,Narang V,Khng J,Lim KC,Sung WK,Sanges R,Stupka E,Oskarsson T,Trumpp A,Wei CL,Müller H,Amati B
Google scholar citations: 1
PLoS Biol 2010 May 11 8 e100038
A large fraction of extragenic RNA pol II transcription sites overlap enhancers.
De Santa F,Barozzi I,Mietton F,Ghisletti S,Polletti S,Tusi BK,Muller H,Ragoussis J,Wei CL,Natoli G
Google scholar citations: 52
Cell Cycle 2010 Dec 1 9 4622-6
TGFß-dependent gene expression shows that senescence correlates with abortive differentiation along several lineages in Myc-induced lymphomas
Müller J,Samans B,van Riggelen J,Fagà G,Peh K N R,Wei CL,Müller H,Amati B,Felsher D,Eilers M
Google scholar citations: 3
Plos One, 2008, Vol. 3 (9), e3178
Identification and analysis of co-occurrence networks with NetCutter
Heiko Muller and Francesco Mancuso
Google scholar citations: 6
Bioinformatics and Biology Insights, 2008, 2, 203–213
Topological properties of co-occurrence networks in published gene expression signatures
Heiko Muller and Francesco Acquati
Nucleic Acids Research, 2007, 35(7), 2343-2355
Identification of cancer signaling pathways from published gene expression signatures using PubLiME.
Giacomo Finocchiaro, Francesco Mattia Mancuso, Heiko Muller
Google scholar citations: 13 (857 downloads)
Nucleic Acids Research, 2007, 35 (5), 1488-1500
Localizing hotspots of antisense transcription
Giacomo Finocchiaro, Maria Stella Carro, Stephanie Francois, Paola Parise, Valentina DiNinni, Heiko Muller
Google scholar citations: 15 (1179 downloads)
Cell Cycle, 2006, Vol. 5, (12), 1331-1341
Lap2a Expression is Controlled by E2F and Deregulated in Various Human Tumors.
Parise, P., G. Finocchiaro, B. Masciadri, M. Quarto, S. Francois, F. Mancuso, and H. Muller.
Google scholar citations: 14
Cell Cycle, 2006, Vol. 5, (11), 1202-1207
DEK Expression is Controlled by E2F and Deregulated in Diverse Tumor Types.
Carro, M.S., F.M. Spiga, M. Quarto, V. Di Ninni, S. Volorio, M. Alcalay, and H. Muller.
Google scholar citations: 45
BMC Bioinformatics, 2005, Vol. 6, Suppl. 4, S14
Mining published lists of cancer related microarray experiments: Identification of a gene expression signature having a critical role in cell-cycle control
Finocchiaro G., Mancuso, F., Muller H.
Google scholar citations: 17
Oncogene, 2005, Vol. 24 (20), 3358-3368
Molecular Signature of Retinoic Acid Treatment in Acute Promyleocytic Leukemia
Meani, N., Minardi, S., Licciulli, S., Gelmetti, V., Lo Coco, F., Nervi, C., Pelicci, P.G., Muller, H., Alcalay, M.
Google scholar citations: 28
Bioinformatics, 2004, Vol. 20 (18), 3670-3672
GenePicker: replicate analysis of Affymetrix gene expression microarrays
Finocchiaro G., Parise P., Minardi S. P., Alcalay M., Muller H.
Google scholar citations: 19
Applied Bioinformatics, 2003, Vol. 2 (4), 245-9
Automated DNA chip annotation tables at IFOM: the importance of sequence databases synchronization and cross-references
Guffanti A, Finocchiaro G, Reid JF, Luzi L, Alcalay M, Confalonieri S, Muller H
Google scholar citations: 4
J. Clin Invest, 2003, Vol 112 (11), 1751-61
Acute Myeloid Leukemia fusion proteins deregulate genes involved in stem cell maintenance and DNA repair
Alcalay M, Meani N, Gelmetti V, Fantozzi A, Fagioli M, Orleth A, Riganelli D, Sebastani C, Cappelli E, Casciari C, Sciurpi MT, Mariano AR, Minardi SP, Luzi L, Muller H, Di Fiore PP, Frosina G and Pelicci PG
Google scholar citations: 131
J Biol Chem 2003 Vol. 278, 46124-37
Identification of Target Genes of the p16INK4A-pRB-E2F Pathway
Vernell R, Helin K, Muller H.
Google scholar citations: 74
Eur J Biochem 2001 Sep;268(18):4969-4978
E2F1-mediated transcriptional inhibition of the plasminogen activator inhibitor type 1 gene.
Koziczak M, Muller H, Helin K, Nagamine Y.
Google scholar citations: 23
Nature Cell Biology 2001 Jun;3(6):552-8 IF:12.0
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
Google scholar citations: 469
Genes Dev. 2001 Feb 1;15(3):267-85.
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.
Google scholar citations: 554
Mol. Cell Biol. 1999; 19(9): 6379 - 6395
CDC25A phosphatase is a target of E2F and is required for efficient E2F induced S phase
Vigo E, Muller H, Prosperini E, Hateboer G, Cartwright P, Moroni C, Helin K
Google scholar citations: 277
Oncogene 1999 Mar 11;18(10):1845-53
The cyclin B2 promoter depends on NF-Y, a trimer whose CCAAT-binding activity is cell-cycle regulated.
Bolognese F, Wasner M, Dohna CL, Gurtner A, Ronchi A, Muller H, Manni I, Mossner J, Piaggio G, Mantovani R, Engeland K
Google scholar citations: 100
Oncogene 1998 Aug 6;17(5):611-623
E2F-6: a novel member of the E2F family is an inhibitor of E2F-dependent transcription.
Cartwright P, Muller H, Wagener C, Holm K, Helin K
Google scholar citations: 148
Mol Cell Biol 1997 Sep;17(9):5508-5520
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
Google scholar citations: 154
Methods Enzymol 1995;254:304-321
Analysis of altered gene expression by differential display.
Liang P, Bauer D, Averboukh L, Warthoe P, Rohrwild M, Muller H, Strauss M, Pardee AB
Google scholar citations: 148
Cancer Res 1995 Feb 15;55(4):949-956
Abnormal patterns of D-type cyclin expression and G1 regulation in human head and neck cancer.
Bartkova J, Lukas J, Muller H, Strauss M, Gusterson B, Bartek J
Google scholar citations: 214
J Cell Biol 1994 May;125(3):625-638
DNA tumor virus oncoproteins and retinoblastoma gene mutations share the ability to relieve the cell's requirement for cyclin D1 function in G1.
Lukas J, Muller H, Bartkova J, Spitkovsky D, Kjerulff AA, Jansen-Durr P, Strauss M, Bartek J
Google scholar citations: 234
Int J Cancer 1994 May 1;57(3):353-361
Cyclin D1 protein expression and function in human breast cancer.
Bartkova J, Lukas J, Muller H, Lutzhoft D, Strauss M, Bartek J
Google scholar citations: 436
Proc Natl Acad Sci U S A 1994 Apr 12;91(8):2945-2949
Cyclin D1 expression is regulated by the retinoblastoma protein.
Muller H, Lukas J, Schneider A, Warthoe P, Bartek J, Eilers M, Strauss M
Google scholar citations: 216
Nucleic Acids Res 1993 Sep 11;21(18):4272-4280
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
Google scholar citations: 609
BOOK CHAPTERS AND REVIEWS
Artificial Intelligence and Heuristic Methods in Bioinformatics
Edited by Paolo Frasconi and Ron Shamir
NATO Science Series
2003, IOS Press, pp 208-223
Near Genome Wide Expression Screening of Tumor Suppressor Pathways using Model Cell Lines with Inducible Transcription Factors - Data Acquisition and Analysis
Heiko Mueller & Myriam Alcalay
Microarrays And Cancer Research,
Edited by Janet A. Warrington, Randy Todd, and David Wong
Biotechniques Press 2002, pp 45-60
Tumor Cell Biology, Cell Lines: Identification of Statistically Robust Gene Expression Patterns in Model Cell Lines and Their Use in Functional Expression Data Mining
Heiko Müller and Myriam Alcalay
Biochim Biophys Acta. 2000 Feb 14;1470(1):M1-12. Review.
The E2F transcription factors: Key regulators of cell proliferation
Heiko Mueller and Kristian Helin
Google scholar citations: 171
Total Google scholar citations: 3664
POSTER PRESENTATIONS
2012 poster BITS 2012: Bioinformatic Italian Society annual meeting
02-04 May, Catania
AnnotateGenomicRegions: A web application
Heiko Muller, Bucci Gabriele, Luca Zammataro
2012 poster BITS 2012: Bioinformatic Italian Society annual meeting
02-04 May, Catania
Integrated Analysis of Epigenetic and Transcriptional Circuits in Gliomagenesis
Gabriele Bucci, Elena Signaroldi, Pasquale Laise, Pierre-Luc Germain, Luca Zammataro, Heiko Muller, Giuseppe Testa
2011 poster BITS 2011: Bioinformatic Italian Society annual meeting
20-22 June, Pisa
Digital Signal Processing of Quantitative Genomic Data.
Cittaro Davide, Bucci Gabriele, Muller Heiko
2011 poster BITS 2011: Bioinformatic Italian Society annual meeting
20-22 June, Pisa
UsingSugarCRM in Streamlining a NGS data-analysis pipeline
Heiko Muller, Gabriele Bucci, Davide Cittaro
2011 poster HITSEQ 2011: Conference on High Throughput Sequencing Analysis and Algorithms, special interest group of
ISMB (Intelligent System for Molecular Biology)
14-16 July, Vienna
Digital Signal Processing of Quantitative Genomic Data.
Cittaro Davide, Bucci Gabriele, Muller Heiko
2007 oral, best poster award
Annual meeting of the Italian Bioinformatics Society (BITS), April 26-28
Naples, Aula Magna Partenope, Via Partenope 36, Italy
“Identification of cancer signaling pathways from published gene expession signatures using PubLiME”
Muller, H.; Mancuso, F.M.; Cittaro, D.; Finocchiaro, G.
2006 oral
Genetics meets Systems Biology: Theory and Practice, November 13-15
Paris, Institut Curie, Amphithéatre Constant Burg, 12 rue Lhomond, France
“Graph-based identification of cancer signaling pathways from published gene expression signatures”
Muller, H.; Mancuso, F.M.; Cittaro, D.; Finocchiaro, G.
2006 poster
Annual meeting of the Italian Bioinformatics Society (BITS), April, 28-29
Bologna, Salone Bolognini, Piazza San Domenico 13, Italy
“Publime: a new tool for meta-analysis of cancer-related microarray experiments”
Finocchiaro, G.; Mancuso, F.M.; Muller, H.
2006 oral
Annual meeting of the Italian Bioinformatics Society (BITS), April 28-29
Bologna, Salone Bolognini, Piazza San Domenico 13, Italy
“Intragenic antisense transcription correlates with long UTRs”
Muller, H.; Parise, P.; Di Ninni, V.; Francois, S.; Carro, M.S.; Finocchiaro, G.
2005 oral by G.F.
Gene Signature Symposia 05
April 13, Aula Magna Univ. of Milan, Milan, Italy
“Mining published lists of cancer related microarray experiments: Identification of a gene signature having a critical role in cell-cycle control.”
Finocchiaro, G.; Mancuso, F.M.; Muller, H.
2005 oral by G.F.
Annual meeting of the Italian Bioinformatics Society (BITS), March 17-19
Milan, Leonardo Da Vinci Congress Center, Via Senigallia 6, Italy
“Mining published lists of cancer related microarray experiments: Identification of a gene signature having a critical role in cell-cycle control.”
Finocchiaro, G.; Mancuso, F.M.; Muller, H.
2004 poster
CNIO Symposium: The Molecular Taxonomy of Cancer, February 3-6
Madrid, Hospital Clínico San Carlos,Spain
“Identification of Target Genes of the p16INK4A-pRB-E2F Pathway”
Richard Vernell, Giacomo Finocchiaro, Kristian Helin, and Heiko Muller
2000 oral
October Workshop on Functional Genomics, Expression Array Technologies and Methods of Analysis, Oct 11-15
Los Angeles, UCLA, Institute for Pure and Applied Mathematics, USA
“Statistically Robust E2F Induced Gene Expression Patterns in Functional Gene Expression Data Mining (Target Gene Bias Analysis)”
Muller, H.; Helin, K.
1998 poster
CSHL Symposium: The Cell Cycle, May 20-24
Cold Spring Harbor Laboratories, Cold Spring Harbor, USA
Identification of direct targets of E2F family members
Vigo, E.; Muller, H.; Cartwright, P.; Helin, K.
1998 poster
Giovanni Armenise – Harvard Foundation 2nd Annual Symposium, June 22-23,
Cape Cod, Chatham Bars Inn, USA
“Analysis of E2F4 phosphorylation”
Muller, H.; Helin, K.
1997 oral
11th European Cell Cycle Conference, April 23-26
Gardone Riviera, Villa Alba, Italy
“Induction of S-phase entry by E2F transcription factors depends on their nuclear localization”
Muller, H.; Moroni, M. C.; Vigo, E.; Petersen, B. O.; Bartek, J.; Helin, K.
1994 oral
CSHL Symposium: The Cell Cycle, May 18-22,
Cold Spring Harbor Laboratories, Cold Spring Harbor, USA
“Cyclin D1 expression is regulated by the retinoblastoma protein”
Muller, H.; Lukas, J.; Schneider, A.; Warthoe, P.; Bartek, J.; Eilers, M.; Strauss, M.
1994 poster
EMBL Conference Oncogenes and Growth Control, April 18-21,
EMBL, Heidelberg, Germany
“Cyclin D1 expression is regulated by the retinoblastoma protein”
Muller, H.; Lukas, J.; Schneider, A.; Warthoe, P.; Bartek, J.; Eilers, M.; Strauss, M.
INVITED PRESENTATIONS
2009 14th January, Norwegian University of Science and Technology, Trondheim, NO
“Decoding the non-coding: Emerging roles of non-coding RNA”
2008 invited seminar
July 18th, The Institute of Cancer Research, London, UK
Meta-analysis of genomic data: Pathway identification using Poisson-binomial
statistics and network partitioning
2007 invited seminar
May 20, Linz, Johannes Kepler University, Institute of Biophysics, Austria
“Identification of cancer signaling pathways by meta-analysis of genomic data”
2006 invited seminar
April 21, Berlin, Humboldt Univ., Inst. Theor. Biol., Invalidenstr. 43, Germany
“Meta-analysis of microarray data: Sense and antisense of mammalian
gene expression”
2005 invited seminar
April 4, Nerviano, Nerviano Medical Sciences, Italy
“Meta-analysis of gene expression microarray data - identification of cancer
genes using Systems Biology and Comparative Genomics approaches”
2005 invited seminar
January 11, University of Warwick, Mathematics Institute, Coventry, UK
“Meta-analysis of gene expression microarray data - identification of cancer
genes using Systems Biology and Comparative Genomics approaches”
2004 invited speaker
Silicon Genetics European Users Conference
September 16-17, Royal Library, London, UK
“Meta-analysis of gene expression microarray data - identification of cancer
genes using Systems Biology and Comparative Genomics approaches”
2004 invited speaker
3rd Arrays Symposium in Research and Diagnosis,
October 29-30, Aarhus University Hospital, Brendstrupgaardvej 100, Denmark
“Meta-analysis of gene expression microarray data - identification of cancer
genes using Systems Biology and Comparative Genomics approaches”
2004 invited seminar
February 12, Institute Mario Negri, Milan, Via La Masa 19, Italy
“From co-regulated genes to cis-regulatory elements in mammalian promoters”
2003 invited seminar
November 18, Brescia, University of Brescia, Dept. Biomedical Sciences
& Biotechnology, viale Europa 11, Italy,
“From co-regulated genes to cis-regulatory motifs in the p16-pRB-E2F
pathway”
2002 invited speaker:
Molecular Genetics of ageing and neoplastic transformation
March 22-28, Alba, Italy,
“High-throughput approaches in biology”
2002 invited speaker:
The Proteomics Congress, May 14-15, London, Café Royal, UK,
“Near genome wide expression screening of the pRB tumor suppressor
pathway”
2002 invited speaker and session chair on pathway informatics:
CHI Symposium on Integrated Bioinformatics: High-throughput interpretation
or Pathways and Biology
January 16-18, Zurich, Swissotel, Switzerland,
“Expression analysis of the pRB tumor suppressor pathway”
2002 invited speaker:
Affymetrix European Seminar Tour
November 4, Rome, Hilton Airport Hotel, Italy
“From co-regulated genes to cis-regulatory motifs in the p16-pRB-E2F
pathway”
2002 invited speaker
Belgian Bioinformatics Conference
April 12, Namur, University of Namur, rue de Bruxelles 61, Namur, Belgium
“Near genome wide expression screening of the pRB tumor suppressor
pathway”
2001 invited speaker
NATO Symposium:
Artificial Intelligence and Heuristic Methods for Bioinformatics
October 1-11, San Miniato, Italy
“Near genome wide expression pattern analysis of the pRB tumor suppressor
pathway”
Heiko Muller
