Andrea Cavalli

60 papers A* 1A 2B 3Journal 47Unranked 6

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Early and Prediagnostic Detection of Pancreatic Cancer from Computed Tomography. CoRR Wenxuan Li, Pedro R. A. S. Bassi, Lizhou Wu, Xinze Zhou, Yuxuan Zhao, Qi Chen, Szymon Plotka, Tianyu Lin, Zheren Zhu, Marisa Martin, Justin Caskey, Shanshan Jiang, Xiaoxi Chen, Jaroslaw B. Cwikla, Artur Sankowski, Yaping Wu, Sergio Decherchi, Andrea Cavalli, Chandana Lall, Cristian Tomasetti, Yaxing Guo, Xuan Yu, Yuqing Cai, Hualin Qiao, Jie Bao, Chenhan Hu, Ximing Wang, Arkadiusz Sitek, Kai Ding, Heng Li, Meiyun Wang, Dexin Yu, Guang Zhang, Yang Yang, Kang Wang, Alan L. Yuille, Zongwei Zhou
2025	J	`jnl`	A tale of two codes: CUDA vs OpenACC for mass-zero constrained dynamics. Int. J. High Perform. Comput. Appl. Alessia Vignolo, Taylor J. Baird, Filippo Spiga, Claudia Canevari, Alessandro Coretti, Rodolphe Vuilleumier, Andrea Cavalli, Sara Bonella, Sergio Decherchi
2025	—	`conf`	AI-Driven CAD for Histological Analysis in Mountain Regions: Advancing Local Healthcare and Sustainable Development. BDAI Matteo Calabrese, Chiara B. Salvemini, Michela Assale, Stefano Sartor, Roberta Patetta, Laura Caramanico, Andrea Cavalli, Stefano Gustincich, Jean Marc Christille
2025	J	`jnl`	Dissecting the RAD51-BRC4 Interaction Landscape through Integrative Molecular Simulations and Experimental Biophysics. J. Chem. Inf. Model. Veronica Bresciani, Francesco Rinaldi, Pedro Franco, Stefania Girotto, Andrea Cavalli, Julian D. Langer, Matteo Masetti, Mattia Bernetti
2025	J	`jnl`	IsoBayes: a Bayesian approach for single-isoform proteomics inference. Bioinform. Jordy Bollon, Michael R. Shortreed, Erin Jeffery, Ben T. Jordan, Rachel Miller, Andrea Cavalli, Lloyd M. Smith, Colin N. Dewey, Gloria M. Sheynkman, Simone Tiberi
2025	—	`conf`	Label Critic: Design Data Before Models. ISBI Pedro R. A. S. Bassi, Qilong Wu, Wenxuan Li, Sergio Decherchi, Andrea Cavalli, Alan L. Yuille, Zongwei Zhou
2025	—	`conf`	Learning Segmentation from Radiology Reports. MICCAI (5) Pedro R. A. S. Bassi, Wenxuan Li, Jieneng Chen, Zheren Zhu, Tianyu Lin, Sergio Decherchi, Andrea Cavalli, Kang Wang, Yang Yang, Alan L. Yuille, Zongwei Zhou
2025	J	`jnl`	Learning Segmentation from Radiology Reports. CoRR Pedro R. A. S. Bassi, Wenxuan Li, Jieneng Chen, Zheren Zhu, Tianyu Lin, Sergio Decherchi, Andrea Cavalli, Kang Wang, Yang Yang, Alan L. Yuille, Zongwei Zhou
2025	J	`jnl`	NanoShaperWeb: Molecular Surface and Pocket Detection Made Visual. J. Chem. Inf. Model. Carlo Abate, Eleonora Serra, Walter Rocchia, Andrea Cavalli, Sergio Decherchi
2025	J	`jnl`	Path-Based Nonequilibrium Binding Free Energy Estimation, from Protein-Ligand to RNA-Ligand Binding. J. Chem. Inf. Model. Eleonora Serra, Alessia Ghidini, Riccardo Aguti, Mattia Bernetti, Sergio Decherchi, Andrea Cavalli
2025	J	`jnl`	RadGPT: Constructing 3D Image-Text Tumor Datasets. CoRR Pedro R. A. S. Bassi, Mehmet Can Yavuz, Kang Wang, Xiaoxi Chen, Wenxuan Li, Sergio Decherchi, Andrea Cavalli, Yang Yang, Alan L. Yuille, Zongwei Zhou
2025	J	`jnl`	Scaling Artificial Intelligence for Multi-Tumor Early Detection with More Reports, Fewer Masks. CoRR Pedro R. A. S. Bassi, Xinze Zhou, Wenxuan Li, Szymon Plotka, Jieneng Chen, Qi Chen, Zheren Zhu, Jakub Przado, Ibrahim E. Hamaci, Sezgin Er, Yuhan Wang, Ashwin Kumar, Björn H. Menze, Jaroslaw B. Cwikla, Yuyin Zhou, Akshay S. Chaudhari, Curtis P. Langlotz, Sergio Decherchi, Andrea Cavalli, Kang Wang, Yang Yang, Alan L. Yuille, Zongwei Zhou
2024	J	`jnl`	AMCG: a graph dual atomic-molecular conditional molecular generator. Mach. Learn. Sci. Technol. Carlo Abate, Sergio Decherchi, Andrea Cavalli
2024	J	`jnl`	Comparing Adiabatic Quantum Computers for satellite images feature extraction. Future Gener. Comput. Syst. Lorenzo Rocutto, Marco Maronese, Daniele Dragoni, Andrea Cavalli, Carlo Cavazzoni
2024	J	`jnl`	Explanation is All You Need in Distillation: Mitigating Bias and Shortcut Learning. CoRR Pedro R. A. S. Bassi, Andrea Cavalli, Sergio Decherchi
2024	J	`jnl`	Faster ISNet for Background Bias Mitigation on Deep Neural Networks. IEEE Access Pedro R. A. S. Bassi, Sergio Decherchi, Andrea Cavalli
2024	J	`jnl`	Faster ISNet for Background Bias Mitigation on Deep Neural Networks. CoRR Pedro R. A. S. Bassi, Sergio Decherchi, Andrea Cavalli
2024	J	`jnl`	Label Critic: Design Data Before Models. CoRR Pedro R. A. S. Bassi, Qilong Wu, Wenxuan Li, Sergio Decherchi, Andrea Cavalli, Alan L. Yuille, Zongwei Zhou
2024	A*	`conf`	Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation? NeurIPS Pedro R. A. S. Bassi, Wenxuan Li, Yucheng Tang, Fabian Isensee, Zifu Wang, Jieneng Chen, Yu-Cheng Chou, Yannick Kirchhoff, Maximilian Rokuss, Ziyan Huang, Jin Ye, Junjun He, Tassilo Wald, Constantin Ulrich, Michael Baumgartner, Saikat Roy, Klaus H. Maier-Hein, Paul F. Jaeger, Yiwen Ye, Yutong Xie, Jianpeng Zhang, Ziyang Chen, Yong Xia, Zhaohu Xing, Lei Zhu, Yousef Sadegheih, Afshin Bozorgpour, Pratibha Kumari, Reza Azad, Dorit Merhof, Pengcheng Shi, Ting Ma, Yuxin Du, Fan Bai, Tiejun Huang, Bo Zhao, Haonan Wang, Xiaomeng Li, Hanxue Gu, Haoyu Dong, Jichen Yang, Maciej A. Mazurowski, Saumya Gupta, Linshan Wu, Jia-Xin Zhuang, Hao Chen, Holger Roth, Daguang Xu, Matthew B. Blaschko, Sergio Decherchi, Andrea Cavalli, Alan L. Yuille, Zongwei Zhou
2024	J	`jnl`	Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation? CoRR Pedro R. A. S. Bassi, Wenxuan Li, Yucheng Tang, Fabian Isensee, Zifu Wang, Jieneng Chen, Yu-Cheng Chou, Yannick Kirchhoff, Maximilian Rokuss, Ziyan Huang, Jin Ye, Junjun He, Tassilo Wald, Constantin Ulrich, Michael Baumgartner, Saikat Roy, Klaus H. Maier-Hein, Paul F. Jaeger, Yiwen Ye, Yutong Xie, Jianpeng Zhang, Ziyang Chen, Yong Xia, Zhaohu Xing, Lei Zhu, Yousef Sadegheih, Afshin Bozorgpour, Pratibha Kumari, Reza Azad, Dorit Merhof, Pengcheng Shi, Ting Ma, Yuxin Du, Fan Bai, Tiejun Huang, Bo Zhao, Haonan Wang, Xiaomeng Li, Hanxue Gu, Haoyu Dong, Jichen Yang, Maciej A. Mazurowski, Saumya Gupta, Linshan Wu, Jiaxin Zhuang, Hao Chen, Holger Roth, Daguang Xu, Matthew B. Blaschko, Sergio Decherchi, Andrea Cavalli, Alan L. Yuille, Zongwei Zhou
2023	J	`jnl`	Assessing the Effectiveness of Non-Turing Computing Paradigms. IEEE Access Lorenzo Rocutto, Marco Maronese, Fabio Lorenzo Traversa, Sergio Decherchi, Andrea Cavalli
2023	J	`jnl`	Molecular Dynamics and Machine Learning Give Insights on the Flexibility-Activity Relationships in Tyrosine Kinome. J. Chem. Inf. Model. Sarmistha Majumdar, Francesco Di Palma, Francesca Spyrakis, Sergio Decherchi, Andrea Cavalli
2021	B	`conf`	An Ab Initio Local Principal Path Algorithm. IJCNN Erika Gardini, Andrea Cavalli, Sergio Decherchi
2021	B	`conf`	On the Stability of Feature Selection in Multiomics Data. IJCNN Luca Pestarino, Giovanni Fiorito, Silvia Polidoro, Paolo Vineis, Andrea Cavalli, Sergio Decherchi
2021	J	`jnl`	Targeting the JAK/STAT Pathway: A Combined Ligand- and Target-Based Approach. J. Chem. Inf. Model. María Gálvez-Llompart, Riccardo Ocello, Laura Rullo, Serena Stamatakos, Irene Alessandrini, Riccardo Zanni, Iñaki Tuñón, Andrea Cavalli, Sanzio Candeletti, Matteo Masetti, Patrizia Romualdi, Maurizio Recanatini
2021	J	`jnl`	Using Principal Paths to Walk Through Music and Visual Art Style Spaces Induced by Convolutional Neural Networks. Cogn. Comput. Erika Gardini, Marco Jacopo Ferrarotti, Andrea Cavalli, Sergio Decherchi
2020	J	`jnl`	Exploring Conformational Dynamics of the Extracellular Venus flytrap Domain of the GABAB Receptor: A Path-Metadynamics Study. J. Chem. Inf. Model. Linn S. M. Evenseth, Riccardo Ocello, Mari Gabrielsen, Matteo Masetti, Maurizio Recanatini, Ingebrigt Sylte, Andrea Cavalli
2020	J	`jnl`	Fast and Memory-Efficient Import Vector Domain Description. Neural Process. Lett. Sergio Decherchi, Andrea Cavalli
2020	J	`jnl`	Spathial: an R package for the evolutionary analysis of biological data. Bioinform. Erika Gardini, Federico M. Giorgi, Sergio Decherchi, Andrea Cavalli
2019	J	`jnl`	Predicting Residence Time and Drug Unbinding Pathway through Scaled Molecular Dynamics. J. Chem. Inf. Model. Doris A. Schuetz, Mattia Bernetti, Martina Bertazzo, Djordje Musil, Hans-Michael Eggenweiler, Maurizio Recanatini, Matteo Masetti, Gerhard F. Ecker, Andrea Cavalli
2018	J	`jnl`	Addendum to BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery. J. Chem. Inf. Model. Sergio Decherchi, Giovanni Bottegoni, Andrea Spitaleri, Walter Rocchia, Andrea Cavalli
2018	J	`jnl`	BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery. J. Chem. Inf. Model. Sergio Decherchi, Giovanni Bottegoni, Andrea Spitaleri, Walter Rocchia, Andrea Cavalli
2018	J	`jnl`	Binding Residence Time through Scaled Molecular Dynamics: A Prospective Application to hDAAO Inhibitors. J. Chem. Inf. Model. Mattia Bernetti, Elena Rosini, Luca Mollica, Matteo Masetti, Loredano Pollegioni, Maurizio Recanatini, Andrea Cavalli
2018	J	`jnl`	Fully Flexible Docking via Reaction-Coordinate-Independent Molecular Dynamics Simulations. J. Chem. Inf. Model. Martina Bertazzo, Mattia Bernetti, Maurizio Recanatini, Matteo Masetti, Andrea Cavalli
2018	—	`conf`	Simple Learning with a Teacher via Biased Regularized Least Squares. LOD Sergio Decherchi, Andrea Cavalli
2017	J	`jnl`	Development of a multisite model for Ni(II) ion in solution from thermodynamic and kinetic data. J. Comput. Chem. Matteo Masetti, Francesco Musiani, Mattia Bernetti, Federico Falchi, Andrea Cavalli, Stefano Ciurli, Maurizio Recanatini
2015	J	`jnl`	A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins. J. Chem. Inf. Model. Francesca Spyrakis, Paolo Benedetti, Sergio Decherchi, Walter Rocchia, Andrea Cavalli, Stefano Alcaro, Francesco Ortuso, Massimo Baroni, Gabriele Cruciani
2015	J	`jnl`	Allosteric Modulation of Alpha7 Nicotinic Receptors: Mechanistic Insight through Metadynamics and Essential Dynamics. J. Chem. Inf. Model. Giovanni Grazioso, Jacopo Sgrignani, Romina Capelli, Carlo Matera, Clelia Dallanoce, Marco De Amici, Andrea Cavalli
2015	J	`jnl`	Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets. PLoS Comput. Biol. Giulia Palermo, Inga Bauer, Pablo Campomanes, Andrea Cavalli, Andrea Armirotti, Stefania Girotto, Ursula Rothlisberger, Marco de Vivo
2015	J	`jnl`	Structure-Based Predictions of Activity Cliffs. J. Chem. Inf. Model. Jarmila Husby, Giovanni Bottegoni, Irina Kufareva, Ruben Abagyan, Andrea Cavalli
2015	J	`jnl`	Unveiling the Atomic-Level Determinants of Acylase-Ligand Complexes: An Experimental and Computational Study. J. Chem. Inf. Model. Luca Mollica, Gianluca Conti, Loredano Pollegioni, Andrea Cavalli, Elena Rosini
2014	J	`jnl`	ALMOST: An all atom molecular simulation toolkit for protein structure determination. J. Comput. Chem. Biao Fu, Aleksandr B. Sahakyan, Carlo Camilloni, Gian Gaetano Tartaglia, Emanuele Paci, Amedeo Caflisch, Michele Vendruscolo, Andrea Cavalli
2014	J	`jnl`	Kinetic Characterization of Fragment Binding in AmpC β-Lactamase by High-Throughput Molecular Simulations. J. Chem. Inf. Model. Paola Bisignano, Stefan Doerr, Matt J. Harvey, Angelo D. Favia, Andrea Cavalli, Gianni De Fabritiis
2014	J	`jnl`	Steered Molecular Dynamics Simulations for Studying Protein-Ligand Interaction in Cyclin-Dependent Kinase 5. J. Chem. Inf. Model. Jagdish Suresh Patel, Anna Berteotti, Simone Ronsisvalle, Walter Rocchia, Andrea Cavalli
2013	J	`jnl`	An Automated Docking Protocol for hERG Channel Blockers. J. Chem. Inf. Model. Giovanni Paolo Di Martino, Matteo Masetti, Luisa Ceccarini, Andrea Cavalli, Maurizio Recanatini
2013	J	`jnl`	Collecting and Assessing Human Lactate Dehydrogenase-A Conformations for Structure-Based Virtual Screening. J. Chem. Inf. Model. Rosa Buonfiglio, Mariarosaria Ferraro, Federico Falchi, Andrea Cavalli, Matteo Masetti, Maurizio Recanatini
2013	—	`ch.`	Ionic Dialysance and Conductivity Modeling. Modelling and Control of Dialysis Systems (2) Francesco Locatelli, Celestina Manzoni, Giuseppe Pontoriero, Andrea Cavalli, Salvatore Di Filippo, Ahmad Taher Azar
2012	J	`jnl`	Combining Dyad Protonation and Active Site Plasticity in BACE-1 Structure-Based Drug Design. J. Chem. Inf. Model. Puneet Kacker, Matteo Masetti, Martina Mangold, Giovanni Bottegoni, Andrea Cavalli
2012	J	`jnl`	In Silico Deconstruction of ATP-Competitive Inhibitors of Glycogen Synthase Kinase-3β. J. Chem. Inf. Model. Paola Bisignano, Chiara Lambruschini, Manuele Bicego, Vittorio Murino, Angelo D. Favia, Andrea Cavalli
2011	—	`conf`	An Innovative Protocol for Comparing Protein Binding Sites via Atomic Grid Maps. KDIR Manuele Bicego, Angelo D. Favia, Paola Bisignano, Andrea Cavalli, Vittorio Murino
2011	J	`jnl`	SERAPhiC: A Benchmark for in Silico Fragment-Based Drug Design. J. Chem. Inf. Model. Angelo D. Favia, Giovanni Bottegoni, Irene Nobeli, Paola Bisignano, Andrea Cavalli
2009	J	`jnl`	Insights into docking and scoring neuronal alpha4beta2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations. J. Comput. Chem. Jacopo Sgrignani, Claudia Bonaccini, Giovanni Grazioso, Matteo Chioccioli, Andrea Cavalli, Paola Gratteri
2008	J	`jnl`	Alpha7 nicotinic acetylcholine receptor agonists: Prediction of their binding affinity through a molecular mechanics Poisson-Boltzmann surface area approach. J. Comput. Chem. Giovanni Grazioso, Andrea Cavalli, Marco De Amici, Maurizio Recanatini, Carlo De Micheli
2008	J	`jnl`	Mechanical Features of J. Chem. Inf. Model. Francesco Colizzi, Maurizio Recanatini, Andrea Cavalli
2008	J	`jnl`	Modeling the hERG potassium channel in a phospholipid bilayer: Molecular dynamics and drug docking studies. J. Comput. Chem. Matteo Masetti, Andrea Cavalli, Maurizio Recanatini
2006	J	`jnl`	A Comparative Study on the Application of Hierarchical-Agglomerative Clustering Approaches to Organize Outputs of Reiterated Docking Runs. J. Chem. Inf. Model. Giovanni Bottegoni, Andrea Cavalli, Maurizio Recanatini
2006	—	`conf`	AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets. ISMB (Supplement of Bioinformatics) Giovanni Bottegoni, Walter Rocchia, Maurizio Recanatini, Andrea Cavalli
2003	B	`conf`	Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform. CCGRID Bennet Uk, Michela Taufer, Thomas Stricker, Giovanni Settanni, Andrea Cavalli, Amedeo Caflisch
2003	A	`conf`	Implementation and Characterization of Protein Folding on a Desktop Computational Grid - Is CHARMM a Suitable Candidate for the United Devices MetaProcessor? IPDPS Bennet Uk, Michela Taufer, Thomas Stricker, Giovanni Settanni, Andrea Cavalli
2002	A	`conf`	Performance Characterization of a Molecular Dynamics Code on PC Clusters: Is There Any Easy Parallelism in CHARMM?. IPDPS Michela Taufer, Egon Perathoner, Andrea Cavalli, Amedeo Caflisch, Thomas Stricker