Papers
Papers with * have alphabetical author order.
Names with * contributed equally.
Names with # share senior co-authorship and/or corresponding co-authorship.
2024
Increased genomic instability and reshaping of tissue microenvironment underlie oncogenic properties of Arid1a mutations.
Alessandro D’Ambrosio, Davide Bressan, Elisa Ferracci, Francesco Carbone, Patrizia Mulè, Federico Rossi, Caterina Barbieri, Elisa Sorrenti, Gaia Fiaccadori, Thomas Detone, Elena Vezzoli, Salvatore Bianchi, Chiara Sartori, Simona Corso, Akihisa Fukuda, Giovanni Bertalot, Andrea Falqui, Mattia Barbareschi, Alessandro Romanel, Diego Pasini, Fulvio Chiacchiera.
Science Advances 2024. [doi]
Germline determinants of aberrant signaling pathways in cancer.
Davide Dalfovo, Riccardo Scandino, Marta Paoli, Samuel Valentini, Alessandro Romanel.
npj Precision Oncology 2024. [doi]
Sterile inflammation via TRPM8 RNA-dependent TLR3-NF-kB/IRF3 activation promotes antitumor immunity in prostate cancer.
Alessandro Alaimo#, Sacha Genovesi, Nicole Annesi, Dario De Felice, Saurav Subedi, Alice Macchia, Federico La Manna, Yari Ciani, Federico Vannuccini, Vera Mugoni, Michela Notarangelo, Michela Libergoli, Francesca Broso, Riccardo Taulli, Ugo Ala, Aurora Savino, Martina Cortese, Somayeh Mirzaaghaei, Valeria Poli, Ian Marc Bonapace, Mauro Giulio Papotti, Luca Molinaro, Claudio Doglioni, Orazio Caffo, Adriano Anesi, Michael Nagler, Giovanni Bertalot, Francesco Giuseppe Carbone, Mattia Barbareschi, Umberto Basso, Erik Dassi, Massimo Pizzato, Alessandro Romanel, Francesca Demichelis, Marianna Kruithof-de Julio, Andrea Lunardi#.
EMBO Journal, 2024. [doi]
Divergent HLA variations and heterogeneous expression but recurrent HLA loss-of- heterozygosity and common HLA-B and TAP transcriptional silencing across advanced pediatric solid cancers.
Wan Ching Lim, Maria Eugenia Marques Da Costa, Karine Godefroy, Eric Jacquet, Loren Gragert, Windy Rondof, Antonin Marchais, Naima Nhiri, Davide Dalfovo, Mathias Viard, Nizar Labaied, Asif M. Khan, Philippe Dessen, Alessandro Romanel, Claudia Pasqualini, Gudrun Schleiermacher, Mary Carrington, Laurence Zitvogel, Jean-Yves Scoazec, Birgit Geoerger#, Jerome Salmon#.
Frontiers in Immunology, 2024. [doi]
2023
Analysis of Genetic Ancestry from NGS Data Using EthSEQ.
Davide Dalfovo, Alessandro Romanel.
Current Protocols, 2023. [doi]
LSD1/PRMT6-targeting gene therapy to attenuate androgen receptor toxic gain-of-function ameliorates spinobulbar muscular atrophy phenotypes in flies and mice.
Ramachandran Prakasam*, Angela Bonadiman*, Roberta Andreotti*, Emanuela Zuccaro, Davide Dalfovo, Caterina Marchioretti, Debasmita Tripathy, Gianluca Petris, Eric N. Anderson, Alice Migazzi, Laura Tosatto, Anna Cereseto, Elena Battaglioli, Gianni Sorarù, Wooi Fang Lim, Carlo Rinaldi, Fabio Sambataro, Naemeh Pourshafie, Christopher Grunseich, Alessandro Romanel, Udai Bhan Pandey, Andrea Contestabile, Giuseppe Ronzitti, Manuela Basso#, Maria Pennuto#
Nature Communications, 2023. [doi]
Synggen: fast and data-driven generation of synthetic heterogeneous NGS cancer data.
Riccardo Scandino, Federico Calabrese, Alessandro Romanel.
Bioinformatics, 2023. [doi]
2022
A slow-cycling/quiescent cells subpopulation is involved in glioma invasiveness.
Francesco Antonica, Lucia Santomaso, Davide Pernici, Linda Petrucci, Giuseppe Aiello, Alessandro Cutarelli, Luciano Conti, Alessandro Romanel, Evelina Miele, Toma Tebaldi, Luca Tiberi.
Nature Communications, 13:4767, 2022. [doi]
Analysis of germline-driven ancestry-associated gene expression in cancers.
Chambwe N, Sayaman RW, Hu D, Huntsman S; Cancer Genome Analysis Network, Kemal A, Caesar-Johnson S, Zenklusen JC, Ziv E, Beroukhim R, Cherniack AD.
STAR Protocol, 3(3):101586, 2022. [doi]
Transient rapamycin treatment during developmental stage extends lifespan in Mus musculus and Drosophila melanogaster.
Giuseppe Aiello*, Cosimo Sabino*, Davide Pernici, Matteo Audano, Francesco Antonica, Matteo Gianesello, Claudio Ballabio, Alessandro Quattrone, Nico Mitro, Alessandro Romanel, Alessia Soldano, Luca Tiberi.
EMBO Reports, 2022. [doi]
Allele-informed copy number evaluation of plasma DNA samples from metastatic prostate cancer patients: the PCF_SELECT consortium assay.
Francesco Orlando, Alessandro Romanel, Blanca Trujillo, Michael Sigouros, Daniel Wetterskog, Orsetta Quaini, Gianmarco Leone, Jenny Z Xiang, Anna Wingate, Scott Tagawa, Anuradha Jayaram, Mark Linch, Mariam Jamal-Hanjani, Charles Swanton, Mark A Rubin, Alexander W Wyatt, Himisha Beltran, Gerhardt Attard#, Francesca Demichelis#.
NAR Cancer, 2022. [doi]
ETS-related gene (ERG) undermines genome stability in mouse prostate progenitors via Gsk3β dependent Nkx3.1 degradation.
Marco Lorenzoni*, Dario De Felice*, Giulia Beccaceci, Giorgia Di Donato, Veronica Foletto, Sacha Genovesi, Arianna Bertossi, Francesco Cambulia, Francesca Lorenzin, Aurora Savino, Lidia Avalle, Alessia Cimadamore, Rodolfo Montironi, Veronica Weber, Francesco Giuseppe Carbone, Mattia Barbareschi, Francesca Demichelis, Alessandro Romanel, Valeria Poli, Giannino Del Sal, Marianna Kruithof-de Julio, Marco Gaspari#, Alessandro Alaimo#, Andrea Lunardi#.
Cancer Letters, 2022. [doi]
Intra-epithelial non-canonical Activin A signaling safeguards prostate progenitor quiescence.
Francesco Cambuli#*, Veronica Foletto*, Alessandro Alaimo, Dario De Felice, Francesco Gandolfi, Maria Dilia Palumbieri, Michela Zaffagni, Sacha Genovesi, Marco Lorenzoni, Martina Celotti, Emiliana Bertossio, Giosuè Mazzero, Arianna Bertossi, Alessandra Bisio, Francesco Berardinelli, Antonio Antoccia, Marco Gaspari, Mattia Barbareschi, Michelangelo Fiorentino, Michael M Shen, Massimo Loda, Alessandro Romanel, Andrea Lunardi.
EMBO Reports, 2022. [doi]
YES1 and MYC amplifications as synergistic resistance mechanisms to different generation ALK-TKIs in advanced NSCLC: brief report of clinical and preclinical proofs.
Roberta Minari, Samuel Valentini, Denise Madeddu, Andrea Cavazzoni, Silvia La Monica, Costanza Anna Maria Lagrasta, Roberto Bertorelli, Veronica De Sanctis, Paola Fassan, Cinzia Azzoni, Lorena Bottarelli, Caterina Frati, Letizia Gnetti, Francesco Facchinetti, Pier Giorgio Petronini, Roberta Alfieri, Alessandro Romanel#, Marcello Tiseo#.
JTO Clinical and Research Reports, 2022. [doi]
Polympact: exploring functional relations among common human genetic variants.
Samuel Valentini, Francesco Gandolfi, Mattia Carolo, Davide Dalfovo, Lara Pozza, Alessandro Romanel.
Nucleic Acids Research, 2022. [doi]
2021
TranSNPs: a class of functional SNPs affecting mRNA translation potential revealed by fraction-based allelic imbalance.
Samuel Valentini*, Caterina Marchioretti*, Alessandra Bisio*, Annalisa Rossi, Sara Zaccara, Alessandro Romanel#, Alberto Inga#.
iScience, 2021. [doi]
Plasma tumor DNA is associated with increased risk of venous thromboembolism in metastatic castration-resistant cancer patients.
Vincenza Conteduca#, Emanuela Scarpi, Daniel Wetterskog, Nicole Brighi, Fabio Ferroni, Alice Rossi, Alessandro Romanel, Giorgia Gurioli, Sara Bleve, Caterina Gianni, Giuseppe Schepisi, Cristian Lolli, Pietro Cortesi, Federica Matteucci, Domenico Barone, Giovanni Paganelli, Francesca Demichelis, Himisha Beltran, Gerhardt Attard, Ugo De Giorgi.
International Journal of Cancer, 2021. [doi]
Analytical protocol to identify local ancestry-associated molecular features in cancer.
Jian Carrot-Zhang#, Seunghun Han, Wanding Zhou, Jeffrey S.Damrauer, Anab Kemal, TCGA Analysis Network, Andrew D.Cherniack#, Rameen Beroukhim#.
STAR Protocols 2 (4), 100766, 2021. [doi]
One-shot analysis of translated mammalian lncRNAs with AHARIBO.
Luca Minati*, Claudia Firrito*, Alessia Del Piano*, Alberto Peretti*, Simone Sidoli, Daniele Peroni, Romina Belli, Francesco Gandolfi, Alessandro Romanel, Paola Bernabo, Jacopo Zasso, Alessandro Quattrone, Graziano Guella, Fabio Lauria, Gabriella Viero, Massimiliano Clamer.
eLife, 2021 [doi]
2020
Calcium cytotoxicity sensitizes prostate cancer cells to standard-of-care treatments for locally advanced tumors.
Alessandro Alaimo, Marco Lorenzoni, Paolo Ambrosino, Arianna Bertossi, Alessandra Bisio, Alice Macchia, Eugenio Zoni, Sacha Genovesi, Francesco Cambuli, Veronica Foletto, Dario De Felice, Maria Virginia Soldovieri, Ilaria Mosca, Francesco Gandolfi, Matteo Brunelli, Gianluca Petris, Anna Cereseto, Alvaro Villarroel, George Thalmann, Francesco Giuseppe Carbone, Marianna Kruithof-de Julio, Mattia Barbareschi, Alessandro Romanel, Maurizio Taglialatela, Andrea Lunardi.
Cell Death & Disease, 11:1039, 2020 [doi]
Exploring functionally annotated transcriptional consensus regulatory elements with CONREL.
Davide Dalfovo, Samuel Valentini, Alessandro Romanel.
Database: The Journal of Biological Databases and Curation, 2020. [doi]
Plasma tumour DNA as an early indicator of treatment response in metastatic castration-resistant prostate cancer.
Vincenza Conteduca, Daniel Wetterskog, Emanuela Scarpi, Alessandro Romanel, Giorgia Gurioli, Anuradha Jayaram, Cristian Lolli, Delila Gasi Tandefelt, Giuseppe Schepisi, Chiara Casadei, Anna Wingate, Federica Matteucci, Giovanni Paganelli, Enrique Gonzalez-Billalabeitia, Francesca Demichelis#, Ugo De Giorgi#, Gerhardt Attard#.
British Journal of Cancer, 2020. [doi]
Ancestry-specific Predisposing Germline Variants in Cancer.
Ninad Oak, Andrew D Cherniack, R Jay Mashl, TCGA Analysis Network, Fred R Hirsch, Li Ding, Rameen Beroukhim, Zeynep H Gümüş, Sharon E Plon, Kuan-Lin Huang.
Genome Medicine, 12(1):51, 2020. [doi]
Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer.
Jian Carrot-Zhang*, Nyasha Chambwe*, Jeffrey S. Damrauer*, Theo A. Knijnenburg*, A. Gordon Robertson*, Christina Yau*, Wanding Zhou*, Ashton C. Berger*, Kuan-lin Huang*, Justin Y. Newberg*, R. Jay Mashl**, Alessandro Romanel**, Rosalyn W. Sayaman**, Francesca Demichelis, Ina Felau, Garrett M. Frampton, Seunghun Han, Katherine A. Hoadley, Anab Kemal, Peter W. Laird, Alexander J. Lazar, Xiuning Le, Ninad Oak, Hui Shen, Christopher K. Wong, Jean C. Zenklusen, Elad Ziv, Cancer Genome Atlas Analysis Network, Andrew D. Cherniack#, Rameen Beroukhim#.
Cancer Cell, 2020. [doi]
Integrative multiplatform molecular profiling of benign prostatic hyperplasia identifies distinct subtypes.
Deli Liu, Jonathan E. Shoag, Daniel Poliak, Ramy S. Goueli, Vaishali Ravikumar, David Redmond, Aram Vosoughi, Jacqueline Fontugne, Heng Pan, Daniel Lee, Domonique Thomas, Keyan Salari, Zongwei Wang, Alessandro Romanel, Alexis Te, Richard Lee, Bilal Chughtai, Aria F. Olumi, Juan Miguel Mosquera, Francesca Demichelis, Olivier Elemento, Mark A. Rubin, Andrea Sboner#, Christopher E. Barbieri#.
Nature Communications, 2020. [doi]
Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer.
Himisha Beltran*#, Alessandro Romanel*#, Vincenza Conteduca, Nicola Casiraghi, Michael Sigouros, Gian Marco Franceschini, Francesco Orlando, Tarcisio Fedrizzi, Sheng-Yu Ku, Emma Dann, Alicia Alonso, Juan Miguel Mosquera, Andrea Sboner, Jenny Xiang, Olivier Elemento, David M. Nanus, Scott T. Tagawa, Matteo Benelli, Francesca Demichelis#.
Journal of Clinical Investigation, 130(4): 1658-1668, 2020. [doi]
Inherited variant in NFκB‐1 promoter is associated with increased risk of IBD in an Algerian population and modulates SOX9 binding.
Imene Hamadou, Sonia Garritano, Alessandro Romanel, Dalila Naimi, Talel Hammada, Francesca Demichelis.
Cancer Reports, e1240, 2020. [doi]
ABEMUS: platform specific and data informed detection of somatic SNVs in cfDNA.
Nicola Casiraghi*, Francesco Orlando*, Yari Ciani, Jenny Xiang, Andrea Sboner, Olivier Elemento, Gerhardt Attard, Himisha Beltran, Francesca Demichelis#, Alessandro Romanel#.
Bioinformatics, 2020. [doi]
2019
PaCBAM: fast and scalable processing of whole exome and targeted sequencing data.
Samuel Valentini, Tarcisio Fedrizzi, Francesca Demichelis, Alessandro Romanel.
BMC Genomics, 20:1018, 2019. [doi]
Truncated BRPF1 Cooperates with Smoothened to Promote Adult Shh Medulloblastoma.
Giuseppe Aiello, Claudio Ballabio, Riccardo Ruggeri, Luca Fagnocchi, Marica Anderle, Ilaria Morassut, Davide Caron, Francesca Garilli, Francesca Gianno, Felice Giangaspero, Silvano Piazza, Alessandro Romanel, Alessio Zippo, Luca Tiberi.
Cell Reports, 4036-4052.e10, 2019. [doi]
Integrative Molecular Analysis of Patients With Advanced and Metastatic Cancer.
Verena Sailer, Kenneth Wa Eng, Tuo Zhang, Rohan Bareja, David J. Pisapia, Alexandros Sigaras, Bhavneet Bhinder, Alessandro Romanel, David Wilkes, Evan Sticca, Joanna Cyrta, Rema Rao, Sheena Sahota, Chantal Pauli, Shaham Beg, Samaneh Motanagh, Myriam Kossai, Jacqueline Fontunge, Loredana Puca, Hanna Rennert, Jenny Zhaoying Xiang, Noah Greco, Rob Kim, Theresa Y. MacDonald, Terra McNary, Mirjam Blattner-Johnson, Marc H. Schiffman, Bishoy M. Faltas, Jeffrey P. Greenfield, David Rickman, Eleni Andreopoulou, Kevin Holcomb, Linda T. Vahdat, Douglas S. Scherr, Koen van Besien, Christopher E. Barbieri, Brian D. Robinson, Howard Alan Fine, Allyson J. Ocean, Ana Molina, Manish A. Shah, David M. Nanus, Qiulu Pan, Francesca Demichelis, Scott T. Tagawa, Wei Song, Juan Miguel Mosquera, Andrea Sboner, Mark A. Rubin, Olivier Elemento, and Himisha Beltran.
JCO Precision Oncology, 2019. [doi]
Third generation EGFR inhibitor osimertinib combined with pemetrexed or cisplatin exerts long-lasting anti-tumor effect in EGFR-mutated pre-clinical models of NSCLC.
Silvia La Monica, Roberta Minari, Daniele Cretella, Lisa Flammini, Claudia Fumarola, Mara Bonelli, Andrea Cavazzoni, Graziana Digiacomo, Maricla Galetti, Denise Madeddu, Angela Falco, Costanza Annamaria Lagrasta, Anna Squadrilli, Elisabetta Barocelli, Alessandro Romanel, Federico Quaini, Pier Giorgio Petronini, Marcello Tiseo# and Roberta Alfieri#.
Journal of Experimental & Clinical Cancer Research, 38:222, 2019. [doi]
Allele-Specific Expression Analysis in Cancer Using Next-Generation Sequencing Data.
Alessandro Romanel.
Cancer Bioinformatics, Methods in Molecular Biology, Springer 1878:125-137, 2019. [doi]
2018
RB1 Heterogeneity in Advanced Metastatic Castration Resistant Prostate Cancer.
Daniel Nava Rodrigues*, Nicola Casiraghi*, Alessandro Romanel, Mateus Crespo, Susana Miranda, Pasquale Rescigno, Ines Figueiredo, Ruth Riisnaes, Suzanne Carreira, Semini Sumanasuriya, Paola Gasperini, Adam Sharp, Joaquin Mateo, Alan Mackay, Christopher McNair, Matthew J Schiewer, Karen E. Knudsen, Gunther Boysen, Francesca Demichelis# and Johann S. de Bono#.
Clinical Cancer Research, 2018. [doi]
A phase II trial of the aurora kinase A inhibitor alisertib for patients with castration resistant and neuroendocrine prostate cancer: efficacy and biomarkers.
Himisha Beltran, Clara Oromendia, Daniel C. Danila, Bruce Montgomery, Christopher Hoimes, Russell Z. Szmulewitz, Ulka Vaishampayan, Andrew J Armstrong, Mark Stein, Jacek Pinski, Juan Miguel Mosquera, Verena Sailer, Rohan Bareja, Alessandro Romanel, Naveen Gumpeni, Andrea Sboner, Etienne Dardenne, Loredana Puca, Davide Prandi, Mark A. Rubin, Howard I. Scher, David S. Rickman, Francesca Demichelis, David M. Nanus, Karla V. Ballman and Scott T Tagawa.
Clinical Cancer Research, 2018. [doi]
Core Biopsies from Prostate Cancer Patients in Active Surveillance Protocols Harbor PTEN and MYC Alterations.
Paolo Gandellini*, Nicola Casiraghi*, Tiziana Rancati, Matteo Benelli, Valentina Doldi, Alessandro Romanel, Maurizio Colecchi, Cristina Marenghi, Riccardo Valdagni, Francesca Demichelis#, Nadia Zaffaroni#.
European Urology Oncology, 2018. [doi]
A highly specific SpCas9 variant is identified by in vivo screening in yeast.
Antonio Casini, Michele Olivieri, Gianluca Petris, Claudia Montagna, Giordano Reginato, Giulia Maule, Francesca Lorenzin, Davide Prandi, Alessandro Romanel, Francesca Demichelis, Alberto Inga, Anna Cereseto.
Nature Biotechnology, 36:265-271, 2018. [doi]
2017
Inherited determinants of early recurrent somatic mutations in prostate cancer.
Alessandro Romanel*, Sonia Garritano*, Blerta Stringa, Mirjam Blattner, Davide Dalfovo, Dimple Chakravarty, David Soong, Kellie A. Cotter, Gianluca Petris, Priyanka Dhingra, Paola Gasperini, Anna Cereseto, Olivier Elemento, Andrea Sboner, Ekta Khurana, Alberto Inga, Mark A. Rubin, Francesca Demichelis.
Nature Communications, 8:48, 2017. [doi] [highlight in Nature Reviews Urology]
Hit and go CAS9 delivered through a lentiviral based self-limiting circuit.
Gianluca Petris, Antonio Casini, Claudia Montagna, Francesca Lorenzin, Davide Prandi, Alessandro Romanel, Jacopo Zasso, Luciano Conti, Francesca Demichelis, Anna Cereseto.
Nature Communications, 8:15334, 2017. [doi]
Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations.
Franklin W. Huang, Juan Miguel Mosquera, Andrea Garofalo, Coyin Oh, Maria Baco, Ali Amin Mansour, Bokang Rabasha,Samira Bahl, Stephanie A. Mullane, Brian D. Robinson, Saud Aldubayan, Francesca Khani, Beerinder Karir, Eejung Kim,Jeremy Chimene-Weiss, Matan Hofree, Alessandro Romanel, Joseph R. Osborne, Jong Wook Kim, Gissou Azabdaftari, AnnaWoloszynska-Read, Karen Sfanos, Angelo M. De Marzo, Francesca Demichelis, Stacey Gabriel, Eliezer M. Van Allen, JillMesirov, Pablo Tamayo, Mark A. Rubin, Isaac J. Powell, Levi A. Garraway.
Cancer Discovery, 2017. [doi]
Androgen receptor gene status in plasma DNA associates with worse outcome on enzalutamide or abiraterone for castration-resistant prostate cancer: a multi-institution correlative biomarker study.
Conteduca V, Wetterskog D, Sharabiani MTA, Grande E, Fernandez-Perez MP, Jayaram A, Salvi S, Castellano D, Romanel A, Lolli C, Casadio V, Gurioli G, Amadori D, Font A, Vazquez-Estevez S, González Del Alba A, Mellado B, Fernandez-Calvo O, Méndez-Vidal MJ, Climent MA, Duran I, Gallardo E, Rodriguez A, Santander C, Sáez MI, Puente J, Gasi Tandefelt D, Wingate A, Dearnaley D; PREMIERE Collaborators; Spanish Oncology Genitourinary Group, Demichelis F, De Giorgi U, Gonzalez-Billalabeitia E, Attard G.
Annals of Oncology, 2017 mdx155. [doi]
EthSEQ: ethnicity annotation from whole exome sequencing data.
Alessandro Romanel#, Tuo Zhang, Olivier Elemento, Francesca Demichelis#.
Bioinformatics, 2017 btx165. [doi]
2016
Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care.
Hanna Rennert, Ken Eng, Tuo Zhang, Adrian Tan, Jenny Xiang, Alessandro Romanel, Rob Kim, Wayne Tam, Yen-Chun Liu, Bhavneet Bhinder, Joanna Cytra, Himisha Beltran, Brian Robinson, Juan Miguel Mosquera, Helen Fernandes, Francesca Demichelis, Andrea Sboner, Michael Kluk, Mark A. Rubin#, Olivier Elemento#.
NPJ Genomic Medicine, 1:16019, 2016. [doi]
2015
Plasma AR and abiraterone-resistant prostate cancer.
Alessandro Romanel*, Delila Gasi Tandefelt*, Vincenza Conteduca, Anuradha Jayaram, Nicola Casiraghi, Daniel Wetterskog, Samanta Salvi, Dino Amadori, Zafeiris Zafeiriou, Pasquale Rescigno, Diletta Bianchini, Giorgia Gurioli, Valentina Casadio, Suzanne Carreira, Jane Goodall, Anna Wingate, Roberta Ferraldeschi, Nina Tunariu, Penny Flohr, Ugo De Giorgi, Johann S. de Bono, Francesca Demichelis#, Gerhardt Attard#.
Science Translational Medicine 7, 312re10, 2015. [doi] [focus]
Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response.
Himisha Beltran, Kenneth Eng, Juan Miguel Mosquera, Alexandros Sigaras, Alessandro Romanel, Hanna Rennert, Myriam Kossai, Chantal Pauli, Bishoy Faltas, Jacqueline Fontugne, Kyung Park, Jason Banfelder, Davide Prandi, Neel Madhukar, Tuo Zhang, Jessica Padilla, Noah Greco, Terra J. McNary, Erick Herrscher, David Wilkes, Theresa Y. MacDonald, Hui Xue, Vladimir Vacic, Anne-Katrin Emde, Dayna Oschwald, Adrian Y. Tan, Zhengming Chen, Colin Collins, Martin E. Gleave, Yuzhuo Wang, Dimple Chakravarty, PMarc Schiffman, Robert Kim, Fabien Campagne, Brian D. Robinson, David M. Nanus, Scott T. Tagawa, Jenny Z. Xiang, Agata Smogorzewska, Francesca Demichelis, David S. Rickman, Andrea Sboner, Olivier Elemento, Mark A. Rubin.
Jama Oncology 1(4):466, 2015. [doi]
*On the impact of discreteness and abstractions on modelling noise in gene regulatory networks.
Chiara Bodei, Luca Bortolussi, Davide Chiarugi, Maria Luisa Guerriero, Alberto Policriti, Alessandro Romanel.
Computational Biology and Chemestry 56:98-108, 2015. [doi]
ASEQ: fast allele-specific studies from next-generation sequencing data.
Alessandro Romanel, Sara Lago, Davide Prandi, Andrea Sboner, Francesca Demichelis.
BMC Medical Genomics 8(1):9, 2015. [doi]
In-silico identification and functional validation of allele-dependent AR enhancers.
Sonia Garritano*, Alessandro Romanel*, Yari Ciribilli*, Alessandra Bisio, Antoneta Gavoci, Alberto Inga#, Francesca Demichelis#.
Oncotarget 6(7):4816-4828, 2015. [url]
2014
Tumor clone dynamics in lethal prostate cancer.
Suzanne Carreira*, Alessandro Romanel*, Jane Goodall*, Emily Grist, Roberta Ferraldeschi, Susana Miranda, Davide Prandi, David Lorente, Jean-Sebastien Frenel,Carmel Pezaro, Aurelius Omlin, Daniel Nava Rodrigues, Penelope Flohr, Nina Tunariu, Johann S de Bono, Francesca Demichelis#, Gerhardt Attard#.
Science Translational Medicine 6, 254ra125, 2014. [doi] [focus]
Unraveling the clonal hierarchy of somatic genomic aberrations.
Davide Prandi, Sylvan C Baca, Alessandro Romanel, Christopher E Barbieri, Juan Miguel Mosquera, Jacqueline Fontugne, Himisha Beltran, Andrea Sboner, Levi A Garraway, Mark A Rubin, Francesca Demichelis.
Genome Biology 15:439, 2014. [doi]
*The Spider Calculus: Computing in Active Graphs.
Benjamin C Pierce, Alessandro Romanel, Daniel Wagner. Essays for the Luca Cardelli Fest,
MSR-TR-2014-104, 2014. [url]
2013
Punctuated Evolution of Prostate Cancer Genomes.
Sylvan C. Baca, Davide Prandi, Michael S. Lawrence, Juan Miguel Mosquera, Alessandro Romanel, Yotam Drier, Kyung Park, Naoki Kitabayashi, Theresa Y. MacDonald, Mahmoud Ghandi, Eliezer Van Allen, Gregory V. Kryukov, Andrea Sboner, Jean-Philippe Theurillat, T. David Soong, Elizabeth Nickerson, Daniel Auclair, Ashutosh Tewari, Himisha Beltran, Robert C. Onofrio, Gunther Boysen, Candace Guiducci, Christopher E. Barbieri, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, Gordon Saksena, Douglas Voet, Alex H. Ramos, Wendy Winckler, Michelle Cipicchio, Kristin Ardlie, Philip W. Kantoff, Michael F. Berger, Stacey B. Gabriel, Todd R. Golub, Matthew Meyerson, Eric S. Lander, Olivier Elemento, Gad Getz, Francesca Demichelis#, Mark A. Rubin#, Levi A. Garraway#.
Cell 153(3):666-677, 2013. [pubmed] [doi] [highlight in Nature Reviews Cancer]
Distinct ERG rearrangement prevalence in prostate cancer: higher frequency in young age and in low PSA prostate cancer.
G Schaefer, J-M Mosquera, R Ramoner, K Park, A Romanel, E Steiner, W Horninger, J Bektic, M ladurner-Rennau, MA Rubin, F Demichelis#, H Klocker#.
Prostate Cancer and Prostatic Disease 16:132-138, 2013. [pubmed] [doi] [highlight in Nature Reviews Urology]
2012
Transcriptional regulation is a major controller of cell cycle transition dynamics.
Alessandro Romanel, Lars Juhl Jensen, Luca Cardelli, Attila Csikász-Nagy.
PLoS ONE 7(1) e29716, 2012. [pubmed] [doi] [pdf] [supp]
2011
Evolving Programs to Simulate Molecular Evolution.
Alessandro Romanel.
Newsletter IEEE TCSIM, issue 9, June 2011. [url]
2010
Estimating the divisibility of complex biological networks by sparseness indices.
Tommaso Mazza, Alessandro Romanel, Ferenc Jordán.
Briefings in Bioinformatics 11(3):364-374, © Oxford Journals, 2010. [pubmed] [doi] [bib] [pdf]Self-assembly processes with cooperativity. [bib] [pdf]
Alessandro Romanel.
In Proceedings of 9th Workshop on Process Algebra and Stochastically Timed Activities (PASTA) , 2010.*Programming Biology in BlenX. [doi] [bib] [pdf]
Lorenzo Dematté, Roberto Larcher, Alida Palmisano, Corrado Priami, Alessandro Romanel.
In Systems Biology for Signaling Networks 1:777-820, Ed. Sangdun Choi, © Springer, 2010.*Modelling self-assembly in BlenX. [doi] [bib] [pdf]
Roberto Larcher, Corrado Priami, Alessandro Romanel.
Transactions on Computational Systems Biology XII , LNCS 5945:163-198, © Springer, 2010.Dynamic Biological Modelling: a language-based approach.
Alessandro Romanel.
PhD thesis , University of Trento, 2010. [bib] [pdf] [slides]*The Spider Calculus: Computing in Active Graphs. [bib] [pdf]
Benjamin C. Pierce, Alessandro Romanel, Daniel Wagner.
January 2010.On the Computational Power of BlenX.
Alessandro Romanel, Corrado Priami.
Theoretical Computer Science 411(2):542-565, © Elsevier, 2010. [doi] [bib] [pdf]
2009
Towards a process calculi approach to study the evolution of biological networks. [bib] [pdf]
Alessandro Romanel.
In Proceedings of 8th Workshop on Process Algebra and Stochastically Timed Activities (PASTA) , 2009.*BlenX Static and Dynamic Semantics. [doi] [bib] [pdf]
Corrado Priami, Paola Quaglia, Alessandro Romanel.
In Proceedings of 20th International Conference on Concurrency Theory (CONCUR) , LNCS 5710:37-52, © Springer, 2009.*Exploiting non-Markovian Bio-Processes. [doi] [bib] [pdf]
Ivan Mura, Davide Prandi, Corrado Priami, Alessandro Romanel.
In Proceedings of 7th Workshop on Quantitative Aspects of Programming Languages (QAPL) , ENTCS 253(3):83-98, Elsevier, 2009.*Analyzing various models of Circadian Clock and Cell Cycle coupling. [url] [bib]
Paolo Ballarini, Attila Csikász-Nagy, Adrien Faure, Roberto Larcher, Paola Lecca, Tommaso Mazza, Ivan Mura, Ferenc Jordán, Alida Palmisano, Alessandro Romanel, Sean Sedwards, Heike Siebert, Sylvain Soliman, Denis Thieffry and Judit Zámborszky.
Formal Methods in Molecular Biology , Dagsthul seminar proceedings 09091, 2009.
2008
*Evolving BlenX programs to simulate the evolution of biological networks. [doi] [bib] [pdf]
Lorenzo Dematté, Corrado Priami, Alessandro Romanel, Orkun Soyer.
Theoretical Computer Science 408(1):83-96, © Elsevier, 2008.Varying the level of abstraction in stochastic molecular dynamics models.
Ivan Mura, Alida Palmisano, Sean Sedwards, Lorenzo Dematté, Alessandro Romanel.
Poster, International Conference on Systems Biology (ICSB) 2008 .*The Beta Workbench: a computational tool to study the dynamics of biological systems. [pubmed] [doi] [bib] [pdf]
Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
Briefings in Bioinformatics 9(5):437-449, © Oxford Journals, 2008.*The BlenX Language: A Tutorial. [doi] [bib] [pdf]
Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
In SFM 2008, LNCS 5016:313-365, © Springer, 2008.On the Decidability and Complexity of the Structural Congruence for Beta-binders. [doi] [bib] [pdf]
Alessandro Romanel, Corrado Priami.
Theoretical Computer Science 404(1-2):156-169, © Elsevier, 2008.*Modelling and simulation of biological processes in BlenX. [doi] [bib]
Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
SIGMETRICS Performance Evaluation Review 35:32-39, ACM, 2008.*Simulation of non-Markovian processes in BlenX. [pdf]
Davide Prandi, Corrado Priami, Alessandro Romanel.
COSBI TR-11-2008.
2007
*A Formal and Integrated Framework to Simulate Evolution of Biological Pathways. [doi] [bib]
Lorenzo Dematté, Corrado Priami, Alessandro Romanel, Orkun Soyer.
In Proceedings of International Conference on Computational Methods in Systems Biology (CMSB) , LNBI 4695:106-120, © Springer, 2007.*BetaWB: modelling and simulating biological processes. [bib] [pdf]
Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
In Proceedings of Summer Computer Simulation Conference (SCSC) 2007 .*Effective Index: A formal measure of drug effects. [bib] [pdf]
Lorenzo Dematté, Davide Prandi, Corrado Priami, Alessandro Romanel.
In Proceedings of 2nd Conference Foundations of Systems Biology in Engineering (FOSBE) 2007 .*Modeling Static Biological Compartments with Beta-binders. [doi] [bib] [pdf]
Maria Luisa Guerriero, Corrado Priami, Alessandro Romanel.
In Proceedings of Algebraic Biology, Second International Conference (AB) 2007 , LNCS 4545:247-261, © Springer-Verlag, 2007.*The Decidability of the Structural Congruence for Beta-binders. [doi] [bib]
Corrado Priami, Alessandro Romanel.
In Proceedings of Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC) 2006 , ENTCS 171(2):155-170, Elsevier, 2007.*The Beta Workbench. [pdf]
Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
COSBI TR-03-2007.
2006
Simple Methods for Peak and Valley Detection in Time Series Microarray Data. [doi] [bib] [pdf]
Andrea Sboner, Alessandro Romanel, Andrea Malossini, Federica Ciocchetta, Francesca Demichelis, Ivano Azzini, Enrico Blanzieri, Rossana Dell'Anna.
In Methods of Microarray Data Analysis V, © Springer, 2006.
2005
A Novel Quality Control Procedure for Gene Expression Time Series.
Andrea Sboner, Alessandro Romanel, Andrea Malossini, Francesca Demichelis, Federica Ciocchetta, Marco Stenico, Enrico Blanzieri, Rossana Dell'Anna.
BITS Annual Meeting 2005 .