BARUZZO, GIACOMO
BARUZZO, GIACOMO
Dipartimento di Ingegneria dell'Informazione - DEI
A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression
2017 Lahens, Nicholas F; Ricciotti, Emanuela; Smirnova, Olga; Toorens, Erik; Kim, Eun Ji; Baruzzo, Giacomo; Hayer, Katharina E; Ganguly, Tapan; Schug, Jonathan; Grant, Gregory R
A standardised open science framework for sharing and re-analysing neural data acquired to continuous stimuli
2024 Di Liberto, Giovanni M.; Nidiffer, Aaron; Crosse, Michael J.; Zuk, Nathaniel; Haro, Stephanie; Cantisani, Giorgia; Winchester, Martin M.; Igoe, Aoife; Mccrann, Ross; Chandra, Satwik; Lalor, Edmund C.; Baruzzo, Giacomo
Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results
2022 Baruzzo, Giacomo; Patuzzi, Ilaria; Di Camillo, Barbara
Cellular population dynamics shape the route to human pluripotency
2023 Panariello, Francesco; Gagliano, Onelia; Luni, Camilla; Grimaldi, Antonio; Angiolillo, Silvia; Qin, Wei; Manfredi, Anna; Annunziata, Patrizia; Slovin, Shaked; Vaccaro, Lorenzo; Riccardo, Sara; Bouche, Valentina; Dionisi, Manuela; Salvi, Marcello; Martewicz, Sebastian; Hu, Manli; Cui, Meihua; Stuart, Hannah; Laterza, Cecilia; Baruzzo, Giacomo; Schiebinger, Geoffrey; Di Camillo, Barbara; Cacchiarelli, Davide; Elvassore, Nicola
Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data
2020 Tanevski, Jovan; Nguyen, Thin; Truong, Buu; Karaiskos, Nikos; Eren Ahsen, Mehmet; Zhang, Xinyu; Shu, Chang; Xu, Ke; Liang, Xiaoyu; Hu, Ying; VV Pham, Hoang; Xiaomei, Li; D Le, Thuc; L Tarca, Adi; Bhatti, Gaurav; Romero, Roberto; Karathanasis, Nestoras; Loher, Phillipe; Chen, Yang; Ouyang, Zhengqing; Mao, Disheng; Zhang, Yuping; Zand, Maryam; Ruan, Jianhua; Hafemeister, Christoph; Qiu, Peng; Tran, Duc; Nguyen, Tin; Gabor, Attila; Yu, Thomas; Guinney, Justin; Glaab, Enrico; Krause, Roland; Banda, Peter; SCTC Consortium, Dream; Baruzzo, Giacomo; Cappellato, Marco; Zorzan, Irene; DEL FAVERO, Simone; Schenato, Luca; Vandin, Fabio; DI CAMILLO, Barbara; Gupta, Shruti; Kumar Verma, Ajay; Ahmad, Shandar; Sharma, Ronesh; Vans, Edwin; Sharma, Alok; Patil, Ashwini; Carrea, Alejandra; Alonso, Andres M.; Diambra, Luis; Narsapuram, Vijay; Kaikala, Vinay; Potnuru, Chaitanyam; Kumar, Sunil; Peng, Jiajie; Wang, Xiaoyu; Shang, Xuequn; Livne, Dani; Snir, Tom; Philip, Hagit; Zilberberg, Alona; Efroni, Sol; Reza Hassanzadeh, Hamid; Hassanzadeh, Reihaneh; Jahanshahi, Ghazal; Naddaf-Sh, M-Mahdi; Drayer, Phillip M.; Naddaf-Sh, Sadra; Ben Guebila, Marouen; Wan, Changlin; Cao, Yuchen; Meamardoost, Saber; Papili Gao, Nan; Gunawan, Rudiyanto; Stolovitzky, Gustavo; Rajewsky, Nikolaus; Saez-Rodriguez, Julio; Meyer, Pablo
IDENTIFICATION OF MIRNA AND TARGET GENES IN THE TRANSCRIPTOME ANALYSIS OF CD34+/LIN- CELLS OF PATIENTS WITH CHRONIC MYELOID LEUKEMIA IN THE CHRONIC PHASE AFTER 12 MONTHS OF NILOTINIB THERAPY
2019 Trojani, A; Pungolino, E; Dal Molin, A; Bossi, Le; Rossi, G; D'Adda, M; Perego, A; Elena, C; Turrini, M; Borin, L; Bucelli, C; Malato, S; Carraro, Mc; Spina, F; Latargia, Ml; Artale, S; Spedini, P; Anghilieri, M; Di Camillo, B; Baruzzo, G; De Canal, G; Iurlo, A; Morra, E; Cairoli, R
Identify, quantify and characterize cellular communication from single cell RNA sequencing data with scSeqComm
2022 Baruzzo, Giacomo; Cesaro, Giulia; Di Camillo, Barbara
Investigating differential abundance methods in microbiome data: A benchmark study
2022 Cappellato, Marco; Baruzzo, Giacomo; Di Camillo, Barbara
ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy
2021 Tangaro, Marco; Defazio, Giuseppe; Fosso, Bruno; Licciulli, Vito Flavio; Grillo, Giorgio; Donvito, Giacinto; Lavezzo, Enrico; Baruzzo, Giacomo; Pesole, Graziano; Santamaria, Monica
MAST: a hybrid Multi-Agent Spatio-Temporal model of tumor microenvironment informed using a data-driven approach
2022 Cesaro, Giulia; Milia, Mikele; Baruzzo, Giacomo; Finco, Giovanni; Morandini, Francesco; Lazzarini, Alessio; Alotto, Piergiorgio; da Cunha Carvalho de Miranda, Noel Filipe; Trajanoski, Zlatko; Finotello, Francesca; Di Camillo, Barbara
metaSPARSim: a 16S rRNA gene sequencing count data simulator
2019 Patuzzi, Ilaria; Baruzzo, Giacomo; Losasso, Carmen; Ricci, Antonia; Di Camillo, Barbara
Modeling Microbial Community Networks: Methods and Tools
2021 Cappellato, Marco; Baruzzo, Giacomo; Patuzzi, Ilaria; DI CAMILLO, Barbara
Nilotinib Deregulates Cell Cycle Checkpoints, ABC Transporters Genes and JAK-STAT Signaling Pathway of CD34+/Lin- Cells in Chronic-Phase Chronic Myeloid Leukemia (CP-CML) Patients after 12 Months of Treatment
2018 Alessandra, Trojani; Ester, Pungolino; Giuseppe, Rossi; Mariella, D'Adda; Milena, Lodola; DAL MOLIN, Alessandra; Baruzzo, Giacomo; Alessandra, Perego; Mauro, Turrini; Chiara, Elena; Lorenza Maria Borin, ; Alessandra, Iurlo; Simona, Malato; Francesco, Spina; Maria Luisa Latargia, ; Pierangelo, Spedini; Salvatore, Artale; Michela, Anghilieri; Carraro Maria Cristina, ; Cristina, Bucelli; Gabriella De Canal, ; Enrica, Morra; Roberto, Cairoli
Nilotinib interferes with cell cycle, ABC transporters and JAK-STAT signaling pathway in CD34+/lin- cells of patients with chronic phase chronic myeloid leukemia after 12 months of treatment
2019 Trojani, Alessandra; Pungolino, Ester; Dal Molin, Alessandra; Lodola, Milena; Rossi, Giuseppe; D'Adda, Mariella; Perego, Alessandra; Elena, Chiara; Turrini, Mauro; Borin, Lorenza; Bucelli, Cristina; Malato, Simona; Carraro, Maria Cristina; Spina, Francesco; Latargia, Maria Luisa; Artale, Salvatore; Spedini, Pierangelo; Anghilieri, Michela; Di Camillo, Barbara; Baruzzo, Giacomo; De Canal, Gabriella; Iurlo, Alessandra; Morra, Enrica; Cairoli, Roberto
Nilotinib-induced bone marrow CD34+/lin-Ph+ cells early clearance in newly diagnosed CP-Chronic Myeloid Leukemia: Final report of the PhilosoPhi34 study
2021 Pungolino, Ester; D'Adda, Mariella; De Canal, Gabriella; Trojani, Alessandra; Perego, Alessandra; Elena, Chiara; Lunghi, Francesca; Turrini, Mauro; Borin, Lorenza; Iurlo, Alessandra; Latargia, Maria Luisa; Carraro, Maria Cristina; Spina, Francesco; Artale, Salvatore; Anghilieri, Michela; Molteni, Alfredo; Caramella, Marianna; Baruzzo, Giacomo; Nichelatti, Michele; Di Camillo, Barbara; Cairoli, Roberto
Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene
2018 Sambo, Francesco; Finotello, Francesca; Lavezzo, Enrico; Baruzzo, Giacomo; Masi, Giulia; Peta, Elektra; Falda, Marco; Toppo, Stefano; Barzon, Luisa; Di Camillo, Barbara
Progressive Down Regulation of JAK-STAT, Cell Cycle, and ABC Transporter Genes in CD34+/Lin- Cells of Chronic-Phase Chronic Myeloid Leukemia (CP-CML) Patients at Diagnosis Vs. 12 Months of Nilotinib Treatment Vs. Healthy Subjects
2019 Trojani, Alessandra; Pungolino, Ester; Rossi, Giuseppe; D'Adda, Mariella; Bossi, Luca Emanuele; Baruzzo, Giacomo; Di Camillo, Barbara; Perego, Alessandra; Turrini, Mauro; Elena, Chiara; Borin, Lorenza Maria; Iurlo, Alessandra; Malato, Simona; Spina, Francesco; Latargia, Maria Luisa; Spedini, Pierangelo; Artale, Salvatore; Anghilieri, Michela; Carraro, Maria Cristina; Bucelli, Cristina; De Canal, Gabriella; Morra, Enrica; Cairoli, Roberto
Results and lessons learned from the sbv IMPROVER metagenomics diagnostics for inflammatory bowel disease challenge
2023 Khachatryan, Lusine; Xiang, Yang; Ivanov, Artem; Glaab, Enrico; Graham, Garrett; Granata, Ilaria; Giordano, Maurizio; Maddalena, Lucia; Piccirillo, Marina; Manipur, Ichcha; Baruzzo, Giacomo; Cappellato, Marco; Avot, Batiste; Stan, Adrian; Battey, James; Lo Sasso, Giuseppe; Boue, Stephanie; Ivanov, Nikolai V; Peitsch, Manuel C; Hoeng, Julia; Falquet, Laurent; Di Camillo, Barbara; Guarracino, Mario R; Ulyantsev, Vladimir; Sierro, Nicolas; Poussin, Carine
Role of the Extracytoplasmic Function Sigma Factor SigE in the Stringent Response of Mycobacterium tuberculosis
2023 Baruzzo, Giacomo; Serafini, Agnese; Finotello, Francesca; Sanavia, Tiziana; Cioetto-Mazzabò, Laura; Boldrin, Francesca; Lavezzo, Enrico; Barzon, Luisa; Toppo, Stefano; Provvedi, Roberta; Manganelli, Riccardo; Di Camillo, Barbara
Simulation-based comprehensive benchmarking of RNA-seq aligners
2017 Baruzzo, Giacomo; Hayer, Katharina E; Kim, Eun Ji; DI CAMILLO, Barbara; Fitzgerald, Garret A; Grant, Gregory R.