Francesco Oteri

Oteri F, Sarti E, Nadalin F, Carbone A*. iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families. Nucleic Acids Research. (2022).

Makamte S, Thureau A, Jabrani A, Paquelin A, Plessis A, Sanial M, Rudenko O, Oteri F, Baaden M, Biou V. A large disordered region confers a wide spanning volume to vertebrate Suppressor of Fused as shown in a trans-species solution study. Journal of Structural Biology. pp.107853 (2022).

Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KRei, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MOzorio, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, et al.. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell . (2021).

Vicedomini R, Blachon C, Oteri F, Carbone A*. MyCLADE: a multi-source domain annotation server for sequence functional exploration. Nucleic Acids Research. (2021).

Teppa E, Zea D, Oteri F, Carbone A*. COVTree: Coevolution in OVerlapped sequences by Tree analysis server. Nucleic Acids Research. (2020).

Drillon G, Champeimont R, Oteri F, Fischer G, Carbone A*. Phylogenetic reconstruction based on synteny block and gene adjacencies. Molecular Biology and Evolution. 37(9), pp.2747–2762 (2020).

Oteri F, Nadalin F, Champeimont R, Carbone A*. BIS2Analyzer: a server for coevolution analysis of conserved protein families. Nucleic Acids Research. (2017).

Uguzzoni G, Lovis SJohn, Oteri F, Schug A, Szurmant H, Weigt M. Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis. Proceedings of the National Academy of Sciences. 114, pp.E2662-E2671 (2017).

Nayeem SM, Oteri F, Baaden M, Deep S. Residues of Alpha Helix H3 Determine Distinctive Features of Transforming Growth Factor β3. The Journal of Physical Chemistry B. 121, pp.5483-5498 (2017).

Coucke A, Uguzzoni G, Oteri F, Cocco S, Monasson R, Weigt M. Direct coevolutionary couplings reflect biophysical residue interactions in proteins. The Journal of Chemical Physics. 145, pp.174102-17 (2016).

Biocca S, Iacovelli F, Matarazzo S, Vindigni G, Oteri F, Desideri A, Falconi M. Molecular mechanism of statin-mediated LOX-1 inhibition. Cell Cycle. 14, pp.1583-1595 (2015).

Lee M-Y, Borgiani P, Johansson I, Oteri F, Mkrtchian S, Falconi M, Ingelman-Sundberg M. High warfarin sensitivity in carriers of CYP2C9*35 is determined by the impaired interaction with P450 oxidoreductase. Pharmacogenomics J. 14(4), pp.343-9 (2014).

Iacovelli F, Alves C, Falconi M, Oteri F, de Oliveira CLP, Desideri A. Influence of the single-strand linker composition on the structural/dynamical properties of a truncated octahedral DNA nano-cage family. Walter NG (Eds.). Biopolymers. 101, pp.992–999 (2014).

Oteri F, Baaden M, Lojou E, Sacquin-Mora S. Multiscale simulations give insight into the hydrogen in and out pathways of [NiFe]-hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans. J Phys Chem B. 118(48), pp.13800-11 (2014).

Oteri F, Ciaccafava A, de Poulpiquet A, Baaden M, Lojou E, Sacquin-Mora S. The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes. Phys Chem Chem Phys. 16(23), pp.11318-22 (2014).

Biocca S, Arcangeli T, Tagliaferri E, Testa B, Vindigni G, Oteri F, Giorgi A, Iacovelli F, Novelli G, Desideri A, Falconi M. Simulative and experimental investigation on the cleavage site that generates the soluble human LOX-1. Arch Biochem Biophys. 540(1-2), pp.9-18 (2013).

Di Marino D, Oteri F, Rocca BMorozzo de, D'Annessa I, Falconi M. Mapping multiple potential ATP binding sites on the matrix side of the bovine ADP/ATP carrier by the combined use of MD simulation and docking. J Mol Model. 18(6), pp.2377-86 (2012).

Ciccacci C, Falconi M, Paolillo N, Oteri F, Forte V, Novelli G, Desideri A, Borgiani P. Characterization of a novel CYP2C9 gene mutation and structural bioinformatic protein analysis in a warfarin hypersensitive patient. Pharmacogenet Genomics. 21(6), pp.344-6 (2011).

Vassallo O, Castelli S, Biswas A, Sengupta S, Das PK, D’Annessa I, Oteri F, Leoni A, Tagliatesta P, Majumder HK. Conjugated eicosapentaenoic acid (cEPA) inhibits L. donovani topoisomerase I and has an antiproliferative activity against L. donovani promastigotes. Open Antimicrob. Agents J. 3, pp.23–29 (2011).

Ceci P, Di Cecca G, Falconi M, Oteri F, Zamparelli C, Chiancone E. Effect of the charge distribution along the "ferritin-like" pores of the proteins from the Dps family on the iron incorporation process. J Biol Inorg Chem. 16(6), pp.869-80 (2011).

Oteri F, Falconi M, Chillemi G, Andersen FF, Oliveira CLP, Pedersen JS, Knudsen BR, Desideri A. Simulative Analysis of a Truncated Octahedral DNA Nanocage Family Indicates the Single-Stranded Thymidine Linkers as the Major Player for the Conformational Variability. J. Phys. Chem. C. 115, pp.16819–16827 (2011).

Falconi M, Oteri F, Di Palma F, Pandey S, Battistoni A, Desideri A. Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport. J Comput Aided Mol Des. 25(2), pp.181-94 (2011).

Di Marino D, Oteri F, Rocca BMorozzo De, Chillemi G, Falconi M. ADP/ATP mitochondrial carrier MD simulations to shed light on the structural-dynamical events that, after an additional mutation, restore the function in a pathological single mutant. J Struct Biol. 172(3), pp.225-32 (2010).

Oliveira CLuis Pinto, Juul S, Jørgensen HLaerke, Knudsen B, Tordrup D, Oteri F, Falconi M, Koch J, Desideri A, Pedersen JSkov, Andersen FFaucon, Knudsen BRuth. Structure of nanoscale truncated octahedral DNA cages: variation of single-stranded linker regions and influence on assembly yields. ACS Nano. 4(3), pp.1367-76 (2010).

Castelli S, Campagna A, Vassallo O, Tesauro C, Fiorani P, Tagliatesta P, Oteri F, Falconi M, Majumder HK, Desideri A. Conjugated eicosapentaenoic acid inhibits human topoisomerase IB with a mechanism different from camptothecin. Arch Biochem Biophys. 486(2), pp.103-10 (2009).