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1. Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes

Author

Hafner, Lukas, Gadin, Enzo, Huang, Lei, Frouin, Arthur, Laporte, Fabien, Gaultier, Charlotte, Vieira, Afonso, Maudet, Claire, Varet, Hugo, Moura, Alexandra, Bracq-Dieye, Hélène, Tessaud-Rita, Nathalie, Maury, Mylène, Dazas, Melody, Legendre, Rachel, Gastineau, Pauline, Tsai, Yu-Huan, Coppée, Jean-Yves, Charlier, Caroline, Patin, Etienne, Chikhi, Rayan, Rocha, Eduardo P. C., Leclercq, Alexandre, Disson, Olivier, Aschard, Hugues, and Lecuit, Marc

Published
2024
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5. Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases

Author

d’Humières, Camille, Delavy, Margot, Alla, Laurie, Ichou, Farid, Gauliard, Emilie, Ghozlane, Amine, Levenez, Florence, Galleron, Nathalie, Quinquis, Benoit, Pons, Nicolas, Mullaert, Jimmy, Bridier-Nahmias, Antoine, Condamine, Bénédicte, Touchon, Marie, Rainteau, Dominique, Lamazière, Antonin, Lesnik, Philippe, Ponnaiah, Maharajah, Lhomme, Marie, Sertour, Natacha, Devente, Savannah, Docquier, Jean-Denis, Bougnoux, Marie-Elisabeth, Tenaillon, Olivier, Magnan, Mélanie, Ruppé, Etienne, Grall, Nathalie, Duval, Xavier, Ehrlich, Dusko, Mentré, France, Denamur, Erick, Rocha, Eduardo P. C., Le Chatelier, Emmanuelle, and Burdet, Charles

Published
2024
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10. IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

Author

Camargo, Antonio Pedro, Call, Lee, Roux, Simon, Nayfach, Stephen, Huntemann, Marcel, Palaniappan, Krishnaveni, Ratner, Anna, Chu, Ken, Mukherjeep, Supratim, Reddy, TBK, Chen, I-Min A, Ivanova, Natalia N, Eloe-Fadrosh, Emiley A, Woyke, Tanja, Baltrus, David A, Castañeda-Barba, Salvador, de la Cruz, Fernando, Funnell, Barbara E, Hall, James PJ, Mukhopadhyay, Aindrila, Rocha, Eduardo PC, Stalder, Thibault, Top, Eva, and Kyrpides, Nikos C

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Humans, Metagenome, Metadata, Software, Databases, Genetic, Plasmids, Microbiota, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.

Published
2024

11. Mining Behavioral Patterns for Conformance Diagnostics

Author

Goulart Rocha, Eduardo, van Zelst, Sebastiaan J., van der Aalst, Wil M. P., Goos, Gerhard, Series Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Marrella, Andrea, editor, Resinas, Manuel, editor, Jans, Mieke, editor, and Rosemann, Michael, editor

Published
2024
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12. Precision-Guided Minimization of Arbitrary Declarative Process Models

Author

Goulart Rocha, Eduardo, van der Aalst, Wil M. P., van der Aalst, Wil, Series Editor, Ram, Sudha, Series Editor, Rosemann, Michael, Series Editor, Szyperski, Clemens, Series Editor, Guizzardi, Giancarlo, Series Editor, van der Aa, Han, editor, Bork, Dominik, editor, Schmidt, Rainer, editor, and Sturm, Arnon, editor

Published
2024
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14. Estudo comparativo da leishmaniose tegumentar americana em crianças e adolescentes procedentes das áreas endêmicas de Buriticupu (Maranhão) e Corte de Pedra (Bahia), Brasil

Author

Costa Jackson M.L., Balby Ivelise Theresa A., Rocha Eduardo José S., Silva Antonio Rafael da, Rebêlo José Manuel M., Ferreira Luiz Alves, Gama Mônica Elinor A., Branco Maria dos Remédios F.C., Burattini Marcelo N., and Soares Nivaldo de Jesus S.

Subjects
Leishmaniose tegumentar americana, Crianças, Adolescentes, Buriticupu, Corte de Pedra, Arctic medicine. Tropical medicine, RC955-962
Abstract

Analisou-se o comportamento da LTA em crianças e adolescentes na faixa etária de 0-15 anos, provenientes das áreas endêmicas de Buriticupu (MA) e Corte de Pedra (BA). Nestas regiões, foram cadastrados 214 pacientes no periodo de 1982 a 1993, sendo 78 (36,4%) oriundos de Corte de Pedra e 136 (63,6%) de Buriticupu. Em Corte de Pedra a faixa etária predominante foi de 0-5 anos com 29 (37,2%) casos. Destes, 62% pertenciam ao sexo masculino. Na região de Buriticupu, 88 (64,7%) casos ocorreram na faixa etária de 11-15 anos, sendo 73,8% do sexo masculino. Nas regiões estudadas, houve predomínio da cor parda com 65,4% em Corte de Pedra, e 75% em Buriticupu. Vinte e seis (33,3%) crianças provenientes de Corte de Pedra eram lavradores, sendo o sexo masculino maioria (57,7%), existindo diferença estatística significante (c2 = 11,21 p = 0,05). Vinte e um (80,8%) casos da ocupação lavrador pertenciam a faixa etária de 11-15 anos. Em Buriticupu 37,5% das crianças eram estudantes, destes 30,2% foram lavradores, todos do sexo masculino (c2 = 32,3 p = 0,05). A maioria dos lavradores, 39 (44,3%) casos eram da faixa etária de 11-15 anos. Tanto em Buriticupu como Corte de Pedra houve predomínio da lesão única, 57,7% e 53,7% dos casos, respectivamente. A duração das lesões destacou-se no período de 1 a 3 meses, com 54 (69,2%) casos em Corte de Pedra e 83 (61%) em Buriticupu (c2 = 11,82 p = 0,05). Quanto a localização das lesões, observou-se que nas duas regiões estudadas os MMII foram predominantes com 58,9% em Corte de Pedra e 77,2% em Buriticupu (c2 = 27,9 p = 0,05), havendo maior ocorrência de lesão ulcerada nas duas regiões. IDRM foi positiva em 61 (78,2%) crianças provenientes de Corte de Pedra, não havendo diferença estatística significativa entre as faixas etárias e a positividade do teste (c2 = 0,0669 p = 0,05).

Published
1998

21. Spread of carbapenemase-producing Morganella spp from 2013 to 2021: a comparative genomic study

Author

Bonnin, Rémy A, Creton, Elodie, Perrin, Amandine, Girlich, Delphine, Emeraud, Cecile, Jousset, Agnès B, Duque, Mathilde, Jacquemin, Aymeric, Hopkins, Katie, Bogaerts, Pierre, Glupczynski, Youri, Pfennigwerth, Niels, Gniadkowski, Marek, Hendrickx, Antoni P A, van der Zwaluw, Kim, Apfalter, Petra, Hartl, Rainer, Studentova, Vendula, Hrabak, Jaroslav, Larrouy-Maumus, Gerald, Rocha, Eduardo P C, Naas, Thierry, and Dortet, Laurent

Published
2024
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23. Kit-Net: Self-Supervised Learning to Kit Novel 3D Objects into Novel 3D Cavities

Author

Devgon, Shivin, Ichnowski, Jeffrey, Danielczuk, Michael, Brown, Daniel S., Balakrishna, Ashwin, Joshi, Shirin, Rocha, Eduardo M. C., Solowjow, Eugen, and Goldberg, Ken

Subjects
Computer Science - Robotics, Computer Science - Artificial Intelligence, Computer Science - Computer Vision and Pattern Recognition
Abstract

In industrial part kitting, 3D objects are inserted into cavities for transportation or subsequent assembly. Kitting is a critical step as it can decrease downstream processing and handling times and enable lower storage and shipping costs. We present Kit-Net, a framework for kitting previously unseen 3D objects into cavities given depth images of both the target cavity and an object held by a gripper in an unknown initial orientation. Kit-Net uses self-supervised deep learning and data augmentation to train a convolutional neural network (CNN) to robustly estimate 3D rotations between objects and matching concave or convex cavities using a large training dataset of simulated depth images pairs. Kit-Net then uses the trained CNN to implement a controller to orient and position novel objects for insertion into novel prismatic and conformal 3D cavities. Experiments in simulation suggest that Kit-Net can orient objects to have a 98.9% average intersection volume between the object mesh and that of the target cavity. Physical experiments with industrial objects succeed in 18% of trials using a baseline method and in 63% of trials with Kit-Net. Video, code, and data are available at https://github.com/BerkeleyAutomation/Kit-Net.

Published
2021

29. Polynomial-Time Conformance Checking for Process Trees

Author

Goulart Rocha, Eduardo, van der Aalst, Wil M. P., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Di Francescomarino, Chiara, editor, Burattin, Andrea, editor, Janiesch, Christian, editor, and Sadiq, Shazia, editor

Published
2023
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30. Remote monitoring of pacemakers and defibrillators: Effective and safe in Brazil?

Author

Rocha, Maria Eduarda Quidute Arrais, Lima, Neiberg de Alcantara, Pinho, Luís Gustavo Bastos, Gondim, David Sales Pereira, Miná, Camila Pinto Cavalcante, Rocha, Eduardo Augusto Quidute Arrais, Rocha, Maria Camila Timbó, Nobre, Juvêncio Santos, Pereira, Francisca Tatiana Moreira, Prakash, Preeya, Maia, Fernanda Pimentel Arraes, and Rocha, Eduardo Arrais

Published
2022
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31. The sound of silent RNA in tuberculosis and the lncRNA role on infection

Author

Rocha, Eduardo Fukutani, Vinhaes, Caian Leal, Araújo-Pereira, Mariana, Mota, Tiago Feitosa, Gupte, Akshay N., Kumar, Nathella Pavan, Arriaga, Maria Belen, Sterling, Timothy R., Babu, Subash, Gaikwad, Sanjay, Karyakarte, Rajesh, Mave, Vidya, Kulkarni, Vandana, Paradkar, Mandar, Viswanathan, Vijay, Kornfeld, Hardy, Gupta, Amita, Andrade, Bruno Bezerril, and Queiroz, Artur Trancoso Lopo de

Published
2024
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34. The evolutionary history of the stearoyl-CoA desaturase gene family in vertebrates

Author

Rocha Eduardo, Galante-Oliveira Susana, Gonçalves Odete, Wilson Jonathan M, Castro L Filipe C, and Cunha Isabel

Subjects
Evolution, QH359-425
Abstract

Background Stearoyl-CoA desaturases (SCDs) are key enzymes involved in de novo monounsaturated fatty acid synthesis. They catalyze the desaturation of saturated fatty acyl-CoA substrates at the delta-9 position, generating essential components of phospholipids, triglycerides, cholesterol esters and wax esters. Despite being crucial for interpreting SCDs roles across species, the evolutionary history of the SCD gene family in vertebrates has yet to be elucidated, in particular their isoform diversity, origin and function. This work aims to contribute to this fundamental effort. Results We show here, through comparative genomics and phylogenetics that the SCD gene family underwent an unexpectedly complex history of duplication and loss events. Paralogy analysis hints that SCD1 and SCD5 genes emerged as part of the whole genome duplications (2R) that occurred at the stem of the vertebrate lineage. The SCD1 gene family expanded in rodents with the parallel loss of SCD5 in the Muridae family. The SCD1 gene expansion is also observed in the Lagomorpha although without the SCD5 loss. In the amphibian Xenopus tropicalis we find a single SCD1 gene but not SCD5, though this could be due to genome incompleteness. In the analysed teleost species no SCD5 is found, while the surrounding SCD5-less locus is conserved in comparison to tetrapods. In addition, the teleost SCD1 gene repertoire expanded to two copies as a result of the teleost specific genome duplication (3R). Finally, we describe clear orthologues of SCD1 and SCD5 in the chondrichthian, Scyliorhinus canicula, a representative of the oldest extant jawed vertebrate clade. Expression analysis in S. canicula shows that whilst SCD1 is ubiquitous, SCD5 is mainly expressed in the brain, a pattern which might indicate an evolutionary conserved function. Conclusion We conclude that the SCD1 and SCD5 genes emerged as part of the 2R genome duplications. We propose that the evolutionary conserved gene expression between distinct lineages underpins the importance of SCD activity in the brain (and probably the pancreas), in a yet to be defined role. We argue that an expression independent of an external stimulus, such as diet induced activity, emerged as a novel function in vertebrate ancestry allocated to the SCD5 isoform in various tissues (e.g. brain and pancreas), and it was selectively maintained throughout vertebrate evolution.

Published
2011
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36. Persistence drives gene clustering in bacterial genomes

Author

Rocha Eduardo PC, Fang Gang, and Danchin Antoine

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Gene clustering plays an important role in the organization of the bacterial chromosome and several mechanisms have been proposed to explain its extent. However, the controversies raised about the validity of each of these mechanisms remind us that the cause of this gene organization remains an open question. Models proposed to explain clustering did not take into account the function of the gene products nor the likely presence or absence of a given gene in a genome. However, genomes harbor two very different categories of genes: those genes present in a majority of organisms – persistent genes – and those present in very few organisms – rare genes. Results We show that two classes of genes are significantly clustered in bacterial genomes: the highly persistent and the rare genes. The clustering of rare genes is readily explained by the selfish operon theory. Yet, genes persistently present in bacterial genomes are also clustered and we try to understand why. We propose a model accounting specifically for such clustering, and show that indispensability in a genome with frequent gene deletion and insertion leads to the transient clustering of these genes. The model describes how clusters are created via the gene flux that continuously introduces new genes while deleting others. We then test if known selective processes, such as co-transcription, physical interaction or functional neighborhood, account for the stabilization of these clusters. Conclusion We show that the strong selective pressure acting on the function of persistent genes, in a permanent state of flux of genes in bacterial genomes, maintaining their size fairly constant, that drives persistent genes clustering. A further selective stabilization process might contribute to maintaining the clustering.

Published
2008
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38. A synthesis of bacterial and archaeal phenotypic trait data.

Author

Madin, Joshua S, Nielsen, Daniel A, Brbic, Maria, Corkrey, Ross, Danko, David, Edwards, Kyle, Engqvist, Martin KM, Fierer, Noah, Geoghegan, Jemma L, Gillings, Michael, Kyrpides, Nikos C, Litchman, Elena, Mason, Christopher E, Moore, Lisa, Nielsen, Søren L, Paulsen, Ian T, Price, Nathan D, Reddy, TBK, Richards, Matthew A, Rocha, Eduardo PC, Schmidt, Thomas M, Shaaban, Heba, Shukla, Maulik, Supek, Fran, Tetu, Sasha G, Vieira-Silva, Sara, Wattam, Alice R, Westfall, David A, and Westoby, Mark

Subjects
Bacteria, Archaea, Ecosystem, Phenotype, Genome, Bacterial, Genome, Archaeal
Abstract

A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures in communities and responses of traits along environmental gradients.

Published
2020

46. Focal lymphocytic sialadenitis and ectopic germinal centers in oral reactive lesions and primary Sjögren’s syndrome: a comparative study

Author

Silva, Evânio Vilela, Almeida, Luciana Yamamoto, Bortoletto, Karen Cristine, Quero, Isabela Barbosa, Jacomini, Fernanda Carolina, de Andrade, Bruno Augusto Benevenuto, Silveira, Heitor Albergoni, Duarte, Andressa, Petean, Flávio Calil, Rocha, Eduardo Melani, Ribeiro-Silva, Alfredo, Carlos, Román, and León, Jorge Esquiche

Published
2022
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