Publications

Learning and actioning general principles of cancer cell drug sensitivity

Carli, Francesco; Di Chiaro, Pierluigi; Morelli, Mariangela; Arora, Chakit; Bisceglia, Luisa; De Oliveira Rosa, Natalia; Cortesi, Alice; Franceschi, Sara; Lessi, Francesca; Di Stefano, Anna Luisa; Santonocito, Orazio Santo; Pasqualetti, Francesco; Aretini, Paolo; Miglionico, Pasquale; Diaferia, Giuseppe R.; Giannotti, Fosca; Liò, Pietro; Duran-Frigola, Miquel; Mazzanti, Chiara Maria; Natoli, Gioacchino; Raimondi, Francesco

CellHit: a web server to predict and analyze cancer patients’ drug responsiveness

Francesco Carli, Natalia De Oliveira Rosa, Simon Blotas, Pierluigi Di Chiaro, Luisa Bisceglia, Mariangela Morelli, Francesca Lessi, Anna Luisa Di Stefano, Chiara Maria Mazzanti, Gioacchino Natoli, Francesco Raimondi

The landscape of cancer-rewired GPCR signaling axes

Arora, Chakit; Matic, Marin; Bisceglia, Luisa; Di Chiaro, Pierluigi; De Oliveira Rosa, Natalia; Carli, Francesco; Clubb, Lauren; Amir Nemati Fard, Lorenzo; Kargas, Giorgos; R. Diaferia, Giuseppe; Vukotic, Ranka; Licata Luana; Wu, Guanming; Natoli, Gioacchino; Gutkind, J. Silvio; Raimondi, Francesco

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

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

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

Gpcrome-Wide Analysis Of G-Protein-Coupling Diversity Using A Computational Biology Approach

Matic, Marin; Miglionico, Pasquale; Tatsumi, Manae; Inoue, Asuka; Raimondi, Francesco

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

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

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

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

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

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

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

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.

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.

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

Mapping The Human Genetic Architecture Of Covid-19

Raimondi, F. et al

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

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.

Genetic Mechanisms Of Critical Illness In Covid-19

Raimondi, F. et al

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.

Interconnecting Flexibility, Structural Communication, And Function In Rhogef Oncoproteins

Felline, A.; Belmonte, L.; Raimondi, F.; Bellucci, L.; Fanelli, F.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Precog: Predicting Coupling Probabilities Of G-Protein Coupled Receptors

Singh, G.; Inoue, A.; Gutkind, J. S.; Russell, R. B.; Raimondi, F.

Familial Intrahepatic Cholestasis: New And Wide Perspectives

Vitale, G.; Gitto, S.; Vukotic, R.; Raimondi, F.; Andreone, P.

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.

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.

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.

Studying How Genetic Variants Affect Mechanism In Biological Systems

Raimondi, F.; Russell, R. B.

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.

Structural Determinants Of Constitutive Activation Of Gα Proteins: Transducin As A Paradigm

Felline, A.; Mariani, S.; Raimondi, F.; Bellucci, L.; Fanelli, F.

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.

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.

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.

Structure Network Analysis To Gain Insights Into Gpcr Function

Fanelli, F.; Felline, A.; Raimondi, F.; Seeber, M.

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.

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.

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.

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.

Catching Functional Modes And Structural Communication In Dbl Family Rho Guanine Nucleotide Exchange Factors

Raimondi, F.; Felline, A.; Fanelli, F.

Webpsn: A Web Server For High-Throughput Investigation Of Structural Communication In Biomacromolecules

Seeber, M.; Felline, A.; Raimondi, F.; Mariani, S.; Fanelli, F.

Network Analysis To Uncover The Structural Communication In Gpcrs

Fanelli, F.; Felline, A.; Raimondi, F.

Nucleotide Binding Affects Intrinsic Dynamics And Structural Communication In Ras Gtpases

Fanelli, F.; Raimondi, F.

Quaternary Structure Predictions And Structural Communication Features Of Gpcr Dimers

Fanelli, F.; Seeber, M.; Felline, A.; Casciari, D.; Raimondi, F.

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.

Light On The Structural Communication In Ras Gtpases

Raimondi, F.; Felline, A.; Portella, G.; Orozco, M.; Fanelli, F.

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.

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.

Nucleotide Binding Switches The Information Flow In Ras Gtpases

Raimondi, F.; Portella, G.; Orozco, M.; Fanelli, F.

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.

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.

Deciphering The Deformation Modes Associated With Function Retention And Specialization In Members Of The Ras Superfamily

Raimondi, F.; Orozco, M.; Fanelli, F.

Computational Modeling Of Intramolecular And Intermolecular Communication In Gpcrs

Fanelli, F.; De Benedetti, P. G.; Raimondi, F.; Seeber, M.

Mechanisms Of Inter- And Intramolecular Communication In Gpcrs And G Proteins

Raimondi, F.; Seeber, M.; De Benedetti, P. G.; Fanelli, F.