Alessandra Carbone

Le Moigne T, Sarti E, Nourisson A, Carbone A, Lemaire SD, Henri J. Crystal structure of chloroplast fructose-1,6-bisphosphate aldolase from the green alga Chlamydomonas reinhardtii. Journal of Structural Biology. (2022).

Dequeker C, Mohseni-Behbahani Y, David L, Laine E, Carbone A. From complete cross-docking to partners identification and binding sites predictions. PLOS Computational Biology. 18(1), (2022).

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).

Vicedomini R, Bouly J-P, Laine E, Falciatore A, Carbone A. Multiple probabilistic models extract features from protein sequence data and resolve functional diversity of very different protein families. Molecular Biology and Evolution. 39(4), (2022).

Seoane B, Carbone A. The complexity of protein interactions unravelled from structural disorder. PLoS Computational Biology. 17(1), (2021).

Pérez-Vargas J§, Teppa E§, Amirache F, Boson B, R de Oliveira R, Combet C, Böckmann A, Fusil F, Freitas N, Carbone A*, Cosset FL*. A fusion peptide in preS1 and the human protein-disulfide isomerase ERp57 are involved in HBV membrane fusion process. eLife. (2021).

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, Nadalin F, Combet C, Zea D, David L, Carbone A. Coevolution analysis of amino-acids reveals diversified drug resistance solutions in viral sequences: a case study of hepatitis B virus. Virus Evolution. 6(1), (2020).

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

Corsi F, Lavery R, Laine E, Carbone A. Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties. PLoS Computational Biology. 16(2), (2020).

Laplaza R, Peccati F, Boto R, Quan C, Carbone A, Piquemal J-P, Maday Y, Contreras-García J. NCIPLOT and the analysis of noncovalent interactions using the reduced density gradient. WIREs Computational Molecular Science. (2020).

Boto R, Peccati F, Laplaza R, Quan C, Carbone A, Piquemal J-P, Maday Y, Contreras-García J. NCIPLOT4: fast, robust and quantitative analysis of noncovalent interactions. Journal of Chemical Theory and Computation. pp.4150–4158 (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).

Karami Y, Saighi P, Vanderhaegen R, Gerlier D, Longhi S, Laine E, Carbone A. Predicting substitutions to modulate disorder and stability in coiled-coils. BMC Bioinformatics. 21(573 ), (2020).

David L, Vicedomini R, Richard H, Carbone A. Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A. Bioinformatics. (2020).

Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu R-R, Xu X-M, Shi H, Chang S, Eisenstein M, Karczynska A, Czaplewski C, Lubecka E, Lipska A, Krupa P, Mozolewska M, Golon Ł, Samsonov S, Liwo A, Crivelli S, Pagès G, Karasikov M, Kadukova M, Yan Y, Huang S-Y, Rosell M, Rodríguez-Lumbreras LAngel, Romero-Durana M, Díaz-Bueno L, Fernandez-Recio J, Christoffer C, Terashi G, Shin W-H, Aderinwale T, Subraman SRaghavendr, Kihara D, Kozakov D, Vajda S, Porter K, Padhorny D, Desta I, Beglov D, Ignatov M, Kotelnikov S, Moal IH, Ritchie DW, de Beauchêne IChauvot, Maigret B, Devignes M-D, Echartea MElisa Ruiz, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Cao Y, Shen Y, Baek M, Park T, Woo H, Seok C, Braitbard M, Bitton L, Scheidman-Duhovny D, DapkŪnas J, Olechnovič K, Venclovas Č, Kundrotas PJ, Belkin S, Chakravarty D, Badal VD, Vakser IA, Vreven T, Vangaveti S, Borrman T, et al.. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins: Structure, Function, and BioinformaticsProteins: Structure, Function, and BioinformaticsProteins. (ja), (2019).

Dequeker C, Laine E, Carbone A. Decrypting protein surfaces by combining evolution, geometry and molecular docking. Proteins. (2019).

Laine E, Karami Y, Carbone A. GEMME: A Simple and Fast Global Epistatic Model Predicting Mutational Effects. Molecular Biology and Evolution. (2019).

Lagarde N, Carbone A, Sacquin-Mora S. Hidden partners: Using cross-docking calculations to predict binding sites for proteins with multiple interactions. PROTEINS: Structure, Function, and Bioinformatics. (2018).

Briquet S, Ourimi A, Pionneau C, Bernardes JS, Carbone A, Chardonnet S, Vaquero C. Identification of Plasmodium falciparum nuclear proteins by mass spectrometry and proposed protein annotation. PLoS One. (2018).

Karami Y, Bitard-Feildel T, Laine E, Carbone A. "Infostery” analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations. Scientific Reports. 8(1), (2018).

Raucci R, Laine E, Carbone A. Local Interaction Signal Analysis predicts protein-protein binding affinity. Structure. (2018).

Abdollahi N, Albani A, Anthony E, Baud A, Cardon M, Clerc R, Czernecki D, Conte R, David L, Delaune A, Djerroud S, Fourgoux P, Guiglielmoni N, Laurentie J, Lehmann N, Lochard C, Montagne R, Myrodia V, Opuu V, Parey E, Polit L, Privé S, Quignot C, Ruiz-Cuevas M, Sissoko M, Sompairac N, Vallerix A, Verrecchia V, Delarue M, Guérois R, Ponty Y, Sacquin-Mora S, Carbone A, Froidevaux C, Le Crom S, Lespinet O, Weigt M, Abboud S, Bernardes JS, Bouvier G, Dequeker C, Ferré A, Fuchs P, Lelandais G, Poulain P, Richard H, Schweke H, Laine* E, Lopes* A. Meet-U: Educating through research immersion. PLOS Computational Biology. 14, pp.1-10 (2018).

Ugarte A, Vicedomini R, Bernardes JS, Carbone A. A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling. Microbiome. (2018).