Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project

Authors: Sarah L. Stenton, Melanie C. O’Leary, Gabrielle Lemire, Grace E. VanNoy, Stephanie DiTroia, Vijay S. Ganesh, Emily Groopman, Emily O’Heir, Brian Mangilog, Ikeoluwa Osei-Owusu, Lynn S. Pais, Jillian Serrano, Moriel Singer-Berk, Ben Weisburd, Michael W. Wilson, Christina Austin-Tse, Marwa Abdelhakim, Azza Althagafi, Giulia Babbi, Riccardo Bellazzi, Samuele Bovo, Maria Giulia Carta, Rita Casadio, Pieter-Jan Coenen, Federica De Paoli, Matteo Floris, Manavalan Gajapathy, Robert Hoehndorf, Julius O. B. Jacobsen, Thomas Joseph, Akash Kamandula, Panagiotis Katsonis, Cyrielle Kint, Olivier Lichtarge, Ivan Limongelli, Yulan Lu, Paolo Magni, Tarun Karthik Kumar Mamidi, Pier Luigi Martelli, Marta Mulargia, Giovanna Nicora, Keith Nykamp, Vikas Pejaver, Yisu Peng, Thi Hong Cam Pham, Maurizio S. Podda, Aditya Rao, Ettore Rizzo, Vangala G. Saipradeep, Castrense Savojardo, Peter Schols, Yang Shen, Naveen Sivadasan, Damian Smedley, Dorian Soru, Rajgopal Srinivasan, Yuanfei Sun, Uma Sunderam, Wuwei Tan, Naina Tiwari, Xiao Wang, Yaqiong Wang, Amanda Williams, Elizabeth A. Worthey, Rujie Yin, Yuning You, Daniel Zeiberg, Susanna Zucca, Constantina Bakolitsa, Steven E. Brenner, Stephanie M. Fullerton, Predrag Radivojac, Heidi L. Rehm, Anne O’Donnell-Luria

Source: Human Genomics, Vol 18, Iss 1, Pp 1-25 (2024)

Subject Terms: Rare disease, Genome sequencing, Genome interpretation, Variant prioritization, Best practices, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1479-7364

Access URL: https://doaj.org/article/29fbe7d26d88463789f004c8908aa4a7

A machine learning approach based on ACMG/AMP guidelines for genomic variant classification and prioritization

Authors: Giovanna Nicora, Susanna Zucca, Ivan Limongelli, Riccardo Bellazzi, Paolo Magni

Source: Scientific Reports, Vol 12, Iss 1, Pp 1-12 (2022)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/83f7d1272e444d46892d22b56fb17b9e

ViR: a tool to solve intrasample variability in the prediction of viral integration sites using whole genome sequencing data

Authors: Elisa Pischedda, Cristina Crava, Martina Carlassara, Susanna Zucca, Leila Gasmi, Mariangela Bonizzoni

Source: BMC Bioinformatics, Vol 22, Iss 1, Pp 1-15 (2021)

Subject Terms: Viral integration, Repetitive DNA, Lateral gene transfer, Non-model organisms, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/03d51bf58f4e425a9a81f00fe0ca0cbf

Extracellular Vesicles Derived From Plasma of Patients With Neurodegenerative Disease Have Common Transcriptomic Profiling

Authors: Daisy Sproviero, Stella Gagliardi, Susanna Zucca, Maddalena Arigoni, Marta Giannini, Maria Garofalo, Valentina Fantini, Orietta Pansarasa, Micol Avenali, Matteo Cotta Ramusino, Luca Diamanti, Brigida Minafra, Giulia Perini, Roberta Zangaglia, Alfredo Costa, Mauro Ceroni, Raffaele A. Calogero, Cristina Cereda

Source: Frontiers in Aging Neuroscience, Vol 14 (2022)

Subject Terms: neurodegenerative diseases, extracellular vesicles, RNA-Seq, mRNA, lncRNA, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fnagi.2022.785741/full; https://doaj.org/toc/1663-4365

Access URL: https://doaj.org/article/f8553c4ef248406a902687b6a84b128f

COVID-19 patients and Dementia: Frontal cortex transcriptomic data

Authors: Maria Garofalo, Stella Gagliardi, Susanna Zucca, Cecilia Pandini, Francesca Dragoni, Daisy Sproviero, Orietta Pansarasa, Tino Emanuele Poloni, Valentina Medici, Annalisa Davin, Silvia Damiana Visonà, Matteo Moretti, Antonio Guaita, Mauro Ceroni, Livio Tronconi, Cristina Cereda

Source: Data in Brief, Vol 38, Iss , Pp 107432- (2021)

Subject Terms: SARS-CoV-2, Transcriptomics, Gene expression, Brain, Computer applications to medicine. Medical informatics, R858-859.7, Science (General), Q1-390

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2352340921007149; https://doaj.org/toc/2352-3409

Access URL: https://doaj.org/article/8b4f5c83d9e34ba9ab3b3d0696616b8e

Differential Neuropathology, Genetics, and Transcriptomics in Two Kindred Cases with Alzheimer’s Disease and Lewy Body Dementia

Authors: Ilaria Palmieri, Tino Emanuele Poloni, Valentina Medici, Susanna Zucca, Annalisa Davin, Orietta Pansarasa, Mauro Ceroni, Livio Tronconi, Antonio Guaita, Stella Gagliardi, Cristina Cereda

Source: Biomedicines, Vol 10, Iss 7, p 1687 (2022)

Subject Terms: Alzheimer’s disease, Lewy body dementia, neuropathology, transcriptomics, substantia nigra, hippocampus, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2227-9059/10/7/1687; https://doaj.org/toc/2227-9059

Access URL: https://doaj.org/article/8e3b8554cdd742058aa27a3ce78bf4d2

Re-using biological devices: a model-aided analysis of interconnected transcriptional cascades designed from the bottom-up

Authors: Lorenzo Pasotti, Massimo Bellato, Michela Casanova, Susanna Zucca, Maria Gabriella Cusella De Angelis, Paolo Magni

Source: Journal of Biological Engineering, Vol 11, Iss 1, Pp 1-19 (2017)

Subject Terms: Bottom-up design, Interconnection, Mathematical modelling, Modularity, Cell burden, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13036-017-0090-3; https://doaj.org/toc/1754-1611

Access URL: https://doaj.org/article/6427082beb964a0d96847b5ba0e75ad7

Fermentation of lactose to ethanol in cheese whey permeate and concentrated permeate by engineered Escherichia coli

Authors: Lorenzo Pasotti, Susanna Zucca, Michela Casanova, Giuseppina Micoli, Maria Gabriella Cusella De Angelis, Paolo Magni

Source: BMC Biotechnology, Vol 17, Iss 1, Pp 1-12 (2017)

Subject Terms: Ethanol, Lactose, Fermentation, Escherichia coli, Whey permeate, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12896-017-0369-y; https://doaj.org/toc/1472-6750

Access URL: https://doaj.org/article/48df62aab71941d2855721a588d690a9

Leukocyte Derived Microvesicles as Disease Progression Biomarkers in Slow Progressing Amyotrophic Lateral Sclerosis Patients

Authors: Daisy Sproviero, Sabrina La Salvia, Federico Colombo, Susanna Zucca, Orietta Pansarasa, Luca Diamanti, Alfredo Costa, Luca Lova, Marta Giannini, Stella Gagliardi, Eliana Lauranzano, Michela Matteoli, Mauro Ceroni, Andrea Malaspina, Cristina Cereda

Source: Frontiers in Neuroscience, Vol 13 (2019)

Subject Terms: amyotrophic lateral sclerosis, biomarkers, disease progression, microvesicles, SOD1, TDP-43, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fnins.2019.00344/full; https://doaj.org/toc/1662-453X

Access URL: https://doaj.org/article/7f2193b7619e4891b18e753a21d724ed

Curcumin and Novel Synthetic Analogs in Cell-Based Studies of Alzheimer’s Disease

Authors: Stella Gagliardi, Valentina Franco, Stefano Sorrentino, Susanna Zucca, Cecilia Pandini, Paola Rota, Stefano Bernuzzi, Alfredo Costa, Elena Sinforiani, Orietta Pansarasa, John R. Cashman, Cristina Cereda

Source: Frontiers in Pharmacology, Vol 9 (2018)

Subject Terms: Alzheimer’s disease, curcumins, next generation sequencing, NF-κB, amyloid beta, mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase, Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fphar.2018.01404/full; https://doaj.org/toc/1663-9812

Access URL: https://doaj.org/article/ce92ed03171540f4a57a0651d1eaca8b

Multi-Faceted Characterization of a Novel LuxR-Repressible Promoter Library for Escherichia coli.

Authors: Susanna Zucca, Lorenzo Pasotti, Nicolò Politi, Michela Casanova, Giuliano Mazzini, Maria Gabriella Cusella De Angelis, Paolo Magni

Source: PLoS ONE, Vol 10, Iss 5, p e0126264 (2015)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/27e4d94445b34c9aa0b87c25050e8f28

Correction: Bottom-Up Engineering of Biological Systems through Standard Bricks: A Modularity Study on Basic Parts and Devices.

Authors: Lorenzo Pasotti, Nicolò Politi, Susanna Zucca, Maria Gabriella Cusella De Angelis, Paolo Magni

Source: PLoS ONE, Vol 7, Iss 10 (2012)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3502579; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/490afa32e8564cb4bb8021e47237c8b1

Bottom-up engineering of biological systems through standard bricks: a modularity study on basic parts and devices.

Authors: Lorenzo Pasotti, Nicolò Politi, Susanna Zucca, Maria Gabriella Cusella De Angelis, Paolo Magni

Source: PLoS ONE, Vol 7, Iss 7, p e39407 (2012)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3401228?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/1b4b918721ed497690d4537411aa3f70