Publications
- Expansion: A Webserver To Explore The Functional Consequences Of Protein-Coding Alternative Splice Variants In Cancer Genomics - Arora, Chakit; De Oliveira Rosa, Natalia; Matic, Marin; Cascone, Mariastella; Miglionico, Pasquale; Raimondi, Francesco; Bioinformatics Advances 2023 CROSSREF
- Brain Histone Beta-Hydroxybutyrylation Couples Metabolism With Gene Expression - Cornuti S, Chen S, Lupori L, Finamore F, Carli F, Samad M, Fenizia S, Caldarelli M, Damiani F, Raimondi F, Mazziotti R, Magnan C, Rocchiccioli S, Gastaldelli A, Baldi P, Tognini P; Cell Mol Life Sci 2023 CROSSREF
- Biology-Inspired Graph Neural Network Encodes Reactome And Reveals Biochemical Reactions Of Disease - Joshua G. Burkhart, Guanming Wu, Xubo Song, Francesco Raimondi, Shannon McWeeney, Melissa H. Wong, Youping Deng; Patterns 2023 CROSSREF
- Gpcrome-Wide Analysis Of G-Protein-Coupling Diversity Using A Computational Biology Approach - Matic, Marin; Miglionico, Pasquale; Tatsumi, Manae; Inoue, Asuka; Raimondi, Francesco; Nature Communications 2023 CROSSREF
- Chromosomal Alterations In Sporadic Medullary Thyroid Carcinoma And Correlation With Outcome - Ramone T, Romei C, Ciampi R, Casalini R, Valetto A, Bertini V, Raimondi F, Onoja A, Prete A, Matrone A, Gambale C, Piaggi P, Torregrossa L, Ugolini C, Elisei R; Endocr Relat Cancer 2023 CROSSREF
- The Gpcr-Gαs-Pka Signaling Axis Promotes T Cell Dysfunction And Cancer Immunotherapy Failure - Wu VH, Yung BS, Faraji F, Saddawi-Konefka R, Wang Z, Wenzel AT, Song MJ, Pagadala MS, Clubb LM, Chiou J, Sinha S, Matic M, Raimondi F, Hoang TS, Berdeaux R, Vignali DAA, Iglesias-Bartolome R, Carter H, Ruppin E, Mesirov JP, Gutkind JS; Nature Immunology 2023 CROSSREF
- Structural Communication Between The Gtpase Sec4P And Its Activator Sec2P: Determinants Of Gef Activity And Early Deformations To Nucleotide Release - Felline, Angelo; Raimondi, Francesco; Gentile, Sara; Fanelli, Francesca; Computational And Structural Biotechnology Journal 2022 CROSSREF
- Prometheusdb: An In-Depth Analysis Of The High-Quality Human Methyl-Proteome - Massignani, Enrico; Giambruno, Roberto; Maniaci, Marianna; Nicosia, Luciano; Yadav, Avinash; Cuomo, Alessandro; Raimondi, Francesco; Bonaldi, Tiziana; Molecular & Cellular Proteomics 2022 CROSSREF
- Precogx: Exploring Gpcr Signaling Mechanisms With Deep Protein Representations - Matic, Marin; Singh, Gurdeep; Carli, Francesco; De Oliveira Rosa, Natalia; Miglionico, Pasquale; Magni, Lorenzo; Gutkind, J Silvio; Russell, Robert B; Inoue, Asuka; Raimondi, Francesco; Nucleic Acids Research 2022 CROSSREF
- An Explainable Model Of Host Genetic Interactions Linked To Covid-19 Severity - Onoja, Anthony; Picchiotti, Nicola; Fallerini, Chiara; Baldassarri, Margherita; Fava, Francesca; , ; Multicenter Study, GEN-COVID; Colombo, Francesca; Chiaromonte, Francesca; Renieri, Alessandra; Furini, Simone; Raimondi, Francesco; Communications Biology 2022 CROSSREF
- Employing A Systematic Approach To Biobanking And Analyzing Clinical And Genetic Data For Advancing Covid-19 Research - Daga, Sergio; Fallerini, Chiara; Baldassarri, Margherita; Fava, Francesca; Valentino, Floriana; Doddato, Gabriella; Benetti, Elisa; Furini, Simone; Giliberti, Annarita; Tita, Rossella; Amitrano, Sara; Bruttini, Mirella; Meloni, Ilaria; Pinto, Anna Maria; Raimondi, Francesco; Stella, Alessandra; Biscarini, Filippo; Picchiotti, Nicola; Gori, Marco; Pinoli, Pietro; Ceri, Stefano; Sanarico, Maurizio; Crawley, Francis P.; Birolo, Giovanni; Renieri, Alessandra; Mari, Francesca; Frullanti, Elisa; European Journal Of Human Genetics 2021 CROSSREF
- Rhogap19D Inhibits Cdc42 Laterally To Control Epithelial Cell Shape And Prevent Invasion - Fic, W.; Bastock, R.; Raimondi, F.; Los, E.; Inoue, Y.; Gallop, J. L.; Russell, R. B.; St Johnston, D.; The Journal Of Cell Biology 2021 CROSSREF
- Allosteric Inhibition Of Parkinson’S-Linked Lrrk2 By Constrained Peptides - Helton, Leah G.; Soliman, Ahmed; von Zweydorf, Felix; Kentros, Michalis; Manschwetus, Jascha T.; Hall, Scotty; Gilsbach, Bernd; Ho, Franz Y.; Athanasopoulos, Panagiotis S.; Singh, Ranjan K.; Leclair, Timothy J.; Versées, Wim; Raimondi, Francesco; Herberg, Friedrich W.; Gloeckner, Christian Johannes; Rideout, Hardy; Kortholt, Arjan; Kennedy, Eileen J.; Acs Chemical Biology 2021 CROSSREF
- Cryo-Em Structure Of The Human Mt1–Gi Signaling Complex - Okamoto, Hiroyuki H.; Miyauchi, Hirotake; Inoue, Asuka; Raimondi, Francesco; Tsujimoto, Hirokazu; Kusakizako, Tsukasa; Shihoya, Wataru; Yamashita, Keitaro; Suno, Ryoji; Nomura, Norimichi; Kobayashi, Takuya; Iwata, So; Nishizawa, Tomohiro; Nureki, Osamu; Nature Structural &Amp; Molecular Biology 2021 CROSSREF
- Mapping The Human Genetic Architecture Of Covid-19 - Raimondi, F. et al; Nature 2021 CROSSREF
- Leveraging Biochemical Reactions To Unravel Functional Impacts Of Cancer Somatic Variants Affecting Protein Interaction Interfaces - Raimondi, Francesco; Burkhart, Joshua G; Betts, Matthew J; Russell, Robert B; Wu, Guanming; F1000Research 2021 CROSSREF
- Gαs-Protein Kinase A (Pka) Pathway Signalopathies: The Emerging Genetic Landscape And Therapeutic Potential Of Human Diseases Driven By Aberrant Gαs-Pka Signaling - Ramms, D. J.; Raimondi, F.; Arang, N.; Herberg, F. W.; Taylor, S. S.; Gutkind, J. S.; Pharmacological Reviews 2021 CROSSREF
- Genetic Mechanisms Of Critical Illness In Covid-19 - Raimondi, F. et al; Nature 2020 CROSSREF
- The Effect Of Liraglutide On Β-Blockade For Preventing Variceal Bleeding: A Case Series - Vukotic, R.; Raimondi, F.; Brodosi, L.; Vitale, G.; Petroni, M. L.; Marchesini, G.; Andreone, P.; Annals Of Internal Medicine 2020 CROSSREF
- Interconnecting Flexibility, Structural Communication, And Function In Rhogef Oncoproteins - Felline, A.; Belmonte, L.; Raimondi, F.; Bellucci, L.; Fanelli, F.; Journal Of Chemical Information And Modeling 2019 CROSSREF
- Defective Homologous Recombination Dna Repair As Therapeutic Target In Advanced Chordoma - Groschel, S.; Hubschmann, D.; Raimondi, F.; Horak, P.; Warsow, G.; Frohlich, M.; Klink, B.; Gieldon, L.; Hutter, B.; Kleinheinz, K.; Bonekamp, D.; Marschal, O.; Chudasama, P.; Mika, J.; Groth, M.; Uhrig, S.; Kramer, S.; Heining, C.; Heilig, C. E.; Richter, D.; Reisinger, E.; Pfutze, K.; Eils, R.; Wolf, S.; von Kalle, C.; Brandts, C.; Scholl, C.; Weichert, W.; Richter, S.; Bauer, S.; Penzel, R.; Schrock, E.; Stenzinger, A.; Schlenk, R. F.; Brors, B.; Russell, R. B.; Glimm, H.; Schlesner, M.; Frohling, S.; Nature Communications 2019 CROSSREF
- Illuminating G-Protein-Coupling Selectivity Of Gpcrs - Inoue, A.; Raimondi, F.; Kadji, F. M. N.; Singh, G.; Kishi, T.; Uwamizu, A.; Ono, Y.; Shinjo, Y.; Ishida, S.; Arang, N.; Kawakami, K.; Gutkind, J. S.; Aoki, J.; Russell, R. B.; Cell 2019 CROSSREF
- Understanding The Role Of Genetic Variability In Lrrk2 In Indian Population - Kishore, A.; Ashok Kumar Sreelatha, A.; Sturm, M.; von-Zweydorf, F.; Pihlstrom, L.; Raimondi, F.; Russell, R.; Lichtner, P.; Banerjee, M.; Krishnan, S.; Rajan, R.; Puthenveedu, D. K.; Chung, S. J.; Bauer, P.; Riess, O.; Gloeckner, C. J.; Kruger, R.; Gasser, T.; Sharma, M.; Movement Disorders 2019 CROSSREF
- Auto-Regulation Of Rab5 Gef Activity In Rabex5 By Allosteric Structural Changes, Catalytic Core Dynamics And Ubiquitin Binding - Lauer, J.; Segeletz, S.; Cezanne, A.; Guaitoli, G.; Raimondi, F.; Gentzel, M.; Alva, V.; Habeck, M.; Kalaidzidis, Y.; Ueffing, M.; Lupas, A. N.; Gloeckner, C. J.; Zerial, M.; Elife 2019 CROSSREF
- Genomic And Transcriptomic Changes Complement Each Other In The Pathogenesis Of Sporadic Burkitt Lymphoma - Lopez, C.; Kleinheinz, K.; Aukema, S. M.; Rohde, M.; Bernhart, S. H.; Hubschmann, D.; Wagener, R.; Toprak, U. H.; Raimondi, F.; Kreuz, M.; Waszak, S. M.; Huang, Z.; Sieverling, L.; Paramasivam, N.; Seufert, J.; Sungalee, S.; Russell, R. B.; Bausinger, J.; Kretzmer, H.; Ammerpohl, O.; Bergmann, A. K.; Binder, H.; Borkhardt, A.; Brors, B.; Claviez, A.; Doose, G.; Feuerbach, L.; Haake, A.; Hansmann, M. -L.; Hoell, J.; Hummel, M.; Korbel, J. O.; Lawerenz, C.; Lenze, D.; Radlwimmer, B.; Richter, J.; Rosenstiel, P.; Rosenwald, A.; Schilhabel, M. B.; Stein, H.; Stilgenbauer, S.; Stadler, P. F.; Szczepanowski, M.; Weniger, M. A.; Zapatka, M.; Eils, R.; Lichter, P.; Loeffler, M.; Moller, P.; Trumper, L.; Klapper, W.; Wagner, S.; Richter, G.; Eils, J.; Kerssemakers, J.; Jaeger-Schmidt, C.; Scholz, I.; Borst, C.; Braulke, F.; Dreyling, M.; Eberth, S.; Einsele, H.; Frickhofen, N.; Haas, S.; Karsch, D.; Klepl, N.; Kneba, M.; Lisfeld, J.; Mantovani-Loffler, L.; Ott, G.; Stadler, C.; Staib, P.; Zenz, T.; Kube, D.; Kostezka, U.; Binder, V.; Leich, E.; Nagel, I.; Pischimariov, J.; Schreiber, S.; Vater, I.; Hopp, L.; Langenberger, D.; Rosolowski, M.; Hoffmann, S.; Kuppers, R.; Burkhardt, B.; Schlesner, M.; Siebert, R.; Nature Communications 2019 CROSSREF
- Angpt2 And Nos3 Polymorphisms And Clinical Outcome In Advanced Hepatocellular Carcinoma Patients Receiving Sorafenib - Marisi, G.; Petracci, E.; Raimondi, F.; Faloppi, L.; Foschi, F. G.; Lauletta, G.; Iavarone, M.; Canale, M.; Valgiusti, M.; Neri, L. M.; Ulivi, P.; Orsi, G.; Rovesti, G.; Vukotic, R.; Conti, F.; Cucchetti, A.; Ercolani, G.; Andrikou, K.; Cascinu, S.; Scartozzi, M.; Casadei-Gardini, A.; Cancers 2019 CROSSREF
- Molecular Switch From Myc To Mycn Expression In Myc Protein Negative Burkitt Lymphoma Cases - Mundo, L.; Ambrosio, M. R.; Raimondi, F.; Del Porro, L.; Guazzo, R.; Mancini, V.; Granai, M.; Jim Rocca, B.; Lopez, C.; Bens, S.; Onyango, N.; Nyagol, J.; Abinya, N.; Navari, M.; Ndede, I.; Patel, K.; Paolo Piccaluga, P.; Bob, R.; de Santi, M. M.; Russell, R. B.; Lazzi, S.; Siebert, R.; Stein, H.; Leoncini, L.; Blood Cancer Journal 2019 CROSSREF
- Profiling Of Epigenetic Features In Clinical Samples Reveals Novel Widespread Changes In Cancer - Noberini, R.; Restellini, C.; Savoia, E. O.; Raimondi, F.; Ghiani, L.; Jodice, M. G.; Bertalot, G.; Bonizzi, G.; Capra, M.; Maffini, F. A.; Tagliabue, M.; Ansarin, M.; Lupia, M.; Giordano, M.; Osti, D.; Pelicci, G.; Chiocca, S.; Bonaldi, T.; Cancers 2019 CROSSREF
- Rare, Functional, Somatic Variants In Gene Families Linked To Cancer Genes: Gpcr Signaling As A Paradigm - Raimondi, F.; Inoue, A.; Kadji, F. M. N.; Shuai, N.; Gonzalez, J. -C.; Singh, G.; de la Vega, A. A.; Sotillo, R.; Fischer, B.; Aoki, J.; Gutkind, J. S.; Russell, R. B.; Oncogene 2019 CROSSREF
- Precog: Predicting Coupling Probabilities Of G-Protein Coupled Receptors - Singh, G.; Inoue, A.; Gutkind, J. S.; Russell, R. B.; Raimondi, F.; Nucleic Acids Research 2019 CROSSREF
- Familial Intrahepatic Cholestasis: New And Wide Perspectives - Vitale, G.; Gitto, S.; Vukotic, R.; Raimondi, F.; Andreone, P.; Digestive And Liver Disease 2019 CROSSREF
- The Mutational Landscape Of Burkitt-Like Lymphoma With 11Q Aberration Is Distinct From That Of Burkitt Lymphoma - Wagener, R.; Seufert, J.; Raimondi, F.; Bens, S.; Kleinheinz, K.; Nagel, I.; Ller, J. A.; Thiele, H.; Hubschmann, D.; Kohler, C. W.; Nurnberg, P.; Au-Yeung, R.; Burkhardt, B.; Horn, H.; Leoncini, L.; Jaffe, E. S.; Ott, G.; Rymkiewicz, G.; Schlesner, M.; Russell, R. B.; Klapper, W.; Siebert, R.; Blood 2019 CROSSREF
- Illuminating The Onco-Gpcrome: Novel G Protein-Coupled Receptor-Driven Oncocrine Networks And Targets For Cancer Immunotherapy - Wu, V.; Yeerna, H.; Nohata, N.; Chiou, J.; Harismendy, O.; Raimondi, F.; Inoue, A.; Russell, R. B.; Tamayo, P.; Gutkind, J. S.; Journal Of Biological Chemistry 2019 CROSSREF
- A Small Chaperone Improves Folding And Routing Of Rhodopsin Mutants Linked To Inherited Blindness - Behnen, P.; Felline, A.; Comitato, A.; Di Salvo, M. T.; Raimondi, F.; Gulati, S.; Kahremany, S.; Palczewski, K.; Marigo, V.; Fanelli, F.; Iscience 2018 CROSSREF
- Studying How Genetic Variants Affect Mechanism In Biological Systems - Raimondi, F.; Russell, R. B.; Essays In Biochemistry 2018 CROSSREF
- Cryptogenic Cholestasis In Young And Adults: Atp8B1, Abcb11, Abcb4, And Tjp2 Gene Variants Analysis By High-Throughput Sequencing - Vitale, G.; Gitto, S.; Raimondi, F.; Mattiaccio, A.; Mantovani, V.; Vukotic, R.; D'Errico, A.; Seri, M.; Russell, R. B.; Andreone, P.; Journal Of Gastroenterology 2018 CROSSREF
- Structural Determinants Of Constitutive Activation Of Gα Proteins: Transducin As A Paradigm - Felline, A.; Mariani, S.; Raimondi, F.; Bellucci, L.; Fanelli, F.; Journal Of Chemical Theory And Computation 2017 CROSSREF
- Genetic Variants Affecting Equivalent Protein Family Positions Reflect Human Diversity - Raimondi, F.; Betts, M. J.; Lu, Q.; Inoue, A.; Gutkind, J. S.; Russell, R. B.; Scientific Reports 2017 CROSSREF
- Corrigendum: Insights Into Cancer Severity From Biomolecular Interaction Mechanisms - Raimondi, F.; Singh, G.; Betts, M. J.; Apic, G.; Vukotic, R.; Andreone, P.; Stein, L.; Russell, R. B.; Scientific Reports 2017 CROSSREF
- Small-Molecule Protein-Protein Interaction Inhibitor Of Oncogenic Rho Signaling - Diviani, D.; Raimondi, F.; Del Vescovo, C. D.; Dreyer, E.; Reggi, E.; Osman, H.; Ruggieri, L.; Gonano, C.; Cavin, S.; Box, C. L.; Lenoir, M.; Overduin, M.; Bellucci, L.; Seeber, M.; Fanelli, F.; Cell Chemical Biology 2016 CROSSREF
- Structure Network Analysis To Gain Insights Into Gpcr Function - Fanelli, F.; Felline, A.; Raimondi, F.; Seeber, M.; Biochemical Society Transactions 2016 CROSSREF
- Structural Model Of The Dimeric Parkinson’S Protein Lrrk2 Reveals A Compact Architecture Involving Distant Interdomain Contacts - Guaitoli, G., Raimondi, F., Gilsbach, B. K., Gómez-Llorente, Y., Deyaert, E., Renzi, F., Li, X., Schaffner, A., Jagtap, P. K. A., Boldt, K., & others.; Proceedings Of The National Academy Of Sciences 2016 CROSSREF
- First Model Of Dimeric Lrrk2: The Challenge Of Unrevealing The Structure Of A Multidomain Parkinson'S-Associated Protein - Guaitoli, G.; Gilsbach, B. K.; Raimondi, F.; Gloeckner, C. J.; Biochemical Society Transactions 2016 CROSSREF
- Insights Into Cancer Severity From Biomolecular Interaction Mechanisms - Raimondi, F.; Singh, G.; Betts, M. J.; Apic, G.; Vukotic, R.; Andreone, P.; Stein, L.; Russell, R. B.; Scientific Reports 2016 CROSSREF
- The Intellectual Disability Protein Rab39B Selectively Regulates Glua2 Trafficking To Determine Synaptic Ampar Composition - Mignogna, M. L.; Giannandrea, M.; Gurgone, A.; Fanelli, F.; Raimondi, F.; Mapelli, L.; Bassani, S.; Fang, H.; Van Anken, E.; Alessio, M.; Passafaro, M.; Gatti, S.; Esteban, J. A.; Huganir, R.; D'Adamo, P.; Nature Communications 2015 CROSSREF
- Catching Functional Modes And Structural Communication In Dbl Family Rho Guanine Nucleotide Exchange Factors - Raimondi, F.; Felline, A.; Fanelli, F.; Journal Of Chemical Information And Modeling 2015 CROSSREF
- Webpsn: A Web Server For High-Throughput Investigation Of Structural Communication In Biomacromolecules - Seeber, M.; Felline, A.; Raimondi, F.; Mariani, S.; Fanelli, F.; Bioinformatics 2015 CROSSREF
- Network Analysis To Uncover The Structural Communication In Gpcrs - Fanelli, F.; Felline, A.; Raimondi, F.; Methods In Cell Biology 2013 CROSSREF
- Nucleotide Binding Affects Intrinsic Dynamics And Structural Communication In Ras Gtpases - Fanelli, F.; Raimondi, F.; Current Pharmaceutical Design 2013 CROSSREF
- Quaternary Structure Predictions And Structural Communication Features Of Gpcr Dimers - Fanelli, F.; Seeber, M.; Felline, A.; Casciari, D.; Raimondi, F.; Progress In Molecular Biology And Translational Science 2013 CROSSREF
- Network And Atomistic Simulations Unveil The Structural Determinants Of Mutations Linked To Retinal Diseases - Mariani, S.; Dell'Orco, D.; Felline, A.; Raimondi, F.; Fanelli, F.; Plos Computational Biology 2013 CROSSREF
- Light On The Structural Communication In Ras Gtpases - Raimondi, F.; Felline, A.; Portella, G.; Orozco, M.; Fanelli, F.; Journal Of Biomolecular Structure & Dynamics 2013 CROSSREF
- A Mixed Protein Structure Network And Elastic Network Model Approach To Predict The Structural Communication In Biomolecular Systems: The Pdz2 Domain From Tyrosine Phosphatase 1E As A Case Study - Raimondi, F.; Felline, A.; Seeber, M.; Mariani, S.; Fanelli, F.; Journal Of Chemical Theory And Computation 2013 CROSSREF
- Light On The Structure Of Thromboxane A2 Receptor Heterodimers - Fanelli, F.; Mauri, M.; Capra, V.; Raimondi, F.; Guzzi, F.; Ambrosio, M.; Rovati, G. E.; Parenti, M.; Cellular And Molecular Life Sciences 2011 CROSSREF
- Nucleotide Binding Switches The Information Flow In Ras Gtpases - Raimondi, F.; Portella, G.; Orozco, M.; Fanelli, F.; Plos Computational Biology 2011 CROSSREF
- Software News And Updates Wordom: A User-Friendly Program For The Analysis Of Molecular Structures, Trajectories, And Free Energy Surfaces - Seeber, M.; Felline, A.; Raimondi, F.; Muff, S.; Friedman, R.; Rao, F.; Caflisch, A.; Fanelli, F.; Journal Of Computational Chemistry 2011 CROSSREF
- Superactive Mutants Of Thromboxane Prostanoid Receptor: Functional And Computational Analysis Of An Active Form Alternative To Constitutively Active Mutants - Ambrosio, M.; Fanelli, F.; Brocchetti, S.; Raimondi, F.; Mauri, M.; Rovati, G. E.; Capra, V.; Cellular And Molecular Life Sciences 2010 CROSSREF
- Deciphering The Deformation Modes Associated With Function Retention And Specialization In Members Of The Ras Superfamily - Raimondi, F.; Orozco, M.; Fanelli, F.; Structure 2010 CROSSREF
- Computational Modeling Of Intramolecular And Intermolecular Communication In Gpcrs - Fanelli, F.; De Benedetti, P. G.; Raimondi, F.; Seeber, M.; Current Protein & Peptide Science 2009 CROSSREF
- Mechanisms Of Inter- And Intramolecular Communication In Gpcrs And G Proteins - Raimondi, F.; Seeber, M.; De Benedetti, P. G.; Fanelli, F.; Journal Of The American Chemical Society 2008 CROSSREF
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