Evolutionary signatures of human cancers revealed via genomic analysis of over 35,000 patients

Autor: Diletta Fontana, Ilaria Crespiatico, Valentina Crippa, Federica Malighetti, Matteo Villa, Fabrizio Angaroni, Luca De Sano, Andrea Aroldi, Marco Antoniotti, Giulio Caravagna, Rocco Piazza, Alex Graudenzi, Luca Mologni, Daniele Ramazzotti

Publikováno v: Nature Communications, Vol 14, Iss 1, Pp 1-18 (2023)

Abstract Recurring sequences of genomic alterations occurring across patients can highlight repeated evolutionary processes with significant implications for predicting cancer progression. Leveraging the ever-increasing availability of cancer omics d

Externí odkaz: https://doaj.org/article/2c8ebc0ac2384c04920b0f140fda5e6f

A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing.

Autor: Lucrezia Patruno, Salvatore Milite, Riccardo Bergamin, Nicola Calonaci, Alberto D'Onofrio, Fabio Anselmi, Marco Antoniotti, Alex Graudenzi, Giulio Caravagna

Publikováno v: PLoS Computational Biology, Vol 19, Iss 11, p e1011557 (2023)

Single-cell RNA and ATAC sequencing technologies enable the examination of gene expression and chromatin accessibility in individual cells, providing insights into cellular phenotypes. In cancer research, it is important to consistently analyze these

Externí odkaz: https://doaj.org/article/711143dbbcf84508bb43f4555ba5999a

J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments

Autor: Fabrizio Angaroni, Alessandro Guidi, Gianluca Ascolani, Alberto d’Onofrio, Marco Antoniotti, Alex Graudenzi

Publikováno v: BMC Bioinformatics, Vol 23, Iss 1, Pp 1-19 (2022)

Abstract Background The combined effects of biological variability and measurement-related errors on cancer sequencing data remain largely unexplored. However, the spatio-temporal simulation of multi-cellular systems provides a powerful instrument to

Externí odkaz: https://doaj.org/article/205aa00a157a47be9c7c8bbfe49d3bb6

Variant calling from scRNA-seq data allows the assessment of cellular identity in patient-derived cell lines

Autor: Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Gianluca Ascolani, Isabella Castiglioni, Rocco Piazza, Marco Antoniotti, Alex Graudenzi

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-3 (2022)

Externí odkaz: https://doaj.org/article/f7e2bb216e4940e9967feeddef8220bf

SBML Level 3: an extensible format for the exchange and reuse of biological models

Autor: Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S Malik‐Sheriff, Stuart L Moodie, Ion I Moraru, Chris J Myers, Aurélien Naldi, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Maciej J Swat, Denis Thieffry, Leandro Watanabe, Darren J Wilkinson, Michael L Blinov, Kimberly Begley, James R Faeder, Harold F Gómez, Thomas M Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson L Lister, Daniel Lucio, Eric Mjolsness, Carole J Proctor, Karthik Raman, Nicolas Rodriguez, Clifford A Shaffer, Bruce E Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier‐Schellersheim, Herbert M Sauro, Bernhard Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C Doyle, Michael Hucka, SBML Level 3 Community members, Richard R Adams, Nicholas A Allen, Bastian R Angermann, Marco Antoniotti, Gary D Bader, Jan Červený, Mélanie Courtot, Chris D Cox, Piero Dalle Pezze, Emek Demir, William S Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T Evelo, Christoph Flamm, Ronan MT Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A Harris, Benjamin D Heavner, Ron Henkel, William S Hlavacek, Bin Hu, Daniel R Hyduke, Hidde de Jong, Nick Juty, Peter D Karp, Jonathan R Karr, Douglas B Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T Monteiro, Kedar Nath Natarajan, Poul MF Nielsen, Tramy Nguyen, Alida Palmisano, Jean‐Baptiste Pettit, Thomas Pfau, Robert D Phair, Tomas Radivoyevitch, Johann M Rohwer, Oliver A Ruebenacker, Julio Saez‐Rodriguez, Martin Scharm, Henning Schmidt, Falk Schreiber, Michael Schubert, Roman Schulte, Stuart C Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie I Stefan, Devin P Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel von Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova, Jeremy Zucker

Publikováno v: Molecular Systems Biology, Vol 16, Iss 8, Pp 1-21 (2020)

Abstract Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edi

Externí odkaz: https://doaj.org/article/86e517962df24b21af078b7f951f7487