Search

Your search keyword '"Muñoz-Torres, Monica"' showing total 30 results
Start Over Author "Muñoz-Torres, Monica"
30 results on '"Muñoz-Torres, Monica"'

1. Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)

Author

Toro, Sabrina, Anagnostopoulos, Anna V, Bello, Sue, Blumberg, Kai, Cameron, Rhiannon, Carmody, Leigh, Diehl, Alexander D, Dooley, Damion, Duncan, William, Fey, Petra, Gaudet, Pascale, Harris, Nomi L, Joachimiak, Marcin, Kiani, Leila, Lubiana, Tiago, Munoz-Torres, Monica C, O'Neil, Shawn, Osumi-Sutherland, David, Puig, Aleix, Reese, Justin P, Reiser, Leonore, Robb, Sofia, Ruemping, Troy, Seager, James, Sid, Eric, Stefancsik, Ray, Weber, Magalie, Wood, Valerie, Haendel, Melissa A, and Mungall, Christopher J

Subjects
Computer Science - Artificial Intelligence
Abstract

Background: Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge in an accurate and computable form. However, their construction and maintenance demand substantial resources and necessitate substantial collaboration between domain experts, curators, and ontology experts. We present Dynamic Retrieval Augmented Generation of Ontologies using AI (DRAGON-AI), an ontology generation method employing Large Language Models (LLMs) and Retrieval Augmented Generation (RAG). DRAGON-AI can generate textual and logical ontology components, drawing from existing knowledge in multiple ontologies and unstructured text sources. Results: We assessed performance of DRAGON-AI on de novo term construction across ten diverse ontologies, making use of extensive manual evaluation of results. Our method has high precision for relationship generation, but has slightly lower precision than from logic-based reasoning. Our method is also able to generate definitions deemed acceptable by expert evaluators, but these scored worse than human-authored definitions. Notably, evaluators with the highest level of confidence in a domain were better able to discern flaws in AI-generated definitions. We also demonstrated the ability of DRAGON-AI to incorporate natural language instructions in the form of GitHub issues. Conclusions: These findings suggest DRAGON-AI's potential to substantially aid the manual ontology construction process. However, our results also underscore the importance of having expert curators and ontology editors drive the ontology generation process.

Published
2023
Full Text
View/download PDF

2. KG-Hub -- Building and Exchanging Biological Knowledge Graphs

Author

Caufield, J Harry, Putman, Tim, Schaper, Kevin, Unni, Deepak R, Hegde, Harshad, Callahan, Tiffany J, Cappelletti, Luca, Moxon, Sierra AT, Ravanmehr, Vida, Carbon, Seth, Chan, Lauren E, Cortes, Katherina, Shefchek, Kent A, Elsarboukh, Glass, Balhoff, James P, Fontana, Tommaso, Matentzoglu, Nicolas, Bruskiewich, Richard M, Thessen, Anne E, Harris, Nomi L, Munoz-Torres, Monica C, Haendel, Melissa A, Robinson, Peter N, Joachimiak, Marcin P, Mungall, Christopher J, and Reese, Justin T

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Artificial Intelligence, Computer Science - Machine Learning
Abstract

Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of knowledge graphs is lacking. Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of knowledge graphs. Features include a simple, modular extract-transform-load (ETL) pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial-environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate knowledge graphs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph machine learning, including node embeddings and training of models for link prediction and node classification.

Published
2023

3. A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery

Author

Danis, Daniel, Bamshad, Michael J., Bridges, Yasemin, Caballero-Oteyza, Andrés, Cacheiro, Pilar, Carmody, Leigh C., Chimirri, Leonardo, Chong, Jessica X., Coleman, Ben, Dalgleish, Raymond, Freeman, Peter J., Graefe, Adam S.L., Groza, Tudor, Hansen, Peter, Jacobsen, Julius O.B., Klocperk, Adam, Kusters, Maaike, Ladewig, Markus S., Marcello, Anthony J., Mattina, Teresa, Mungall, Christopher J., Munoz-Torres, Monica C., Reese, Justin T., Rehburg, Filip, Reis, Bárbara C.S., Schuetz, Catharina, Smedley, Damian, Strauss, Timmy, Sundaramurthi, Jagadish Chandrabose, Thun, Sylvia, Wissink, Kyran, Wagstaff, John F., Zocche, David, Haendel, Melissa A., and Robinson, Peter N.

Published
2025
Full Text
View/download PDF

4. A Simple Standard for Sharing Ontological Mappings (SSSOM)

Author

Matentzoglu, Nicolas, Balhoff, James P., Bello, Susan M., Bizon, Chris, Brush, Matthew, Callahan, Tiffany J., Chute, Christopher G, Duncan, William D., Evelo, Chris T., Gabriel, Davera, Graybeal, John, Gray, Alasdair, Gyori, Benjamin M., Haendel, Melissa, Harmse, Henriette, Harris, Nomi L., Harrow, Ian, Hegde, Harshad, Hoyt, Amelia L., Hoyt, Charles T., Jiao, Dazhi, Jiménez-Ruiz, Ernesto, Jupp, Simon, Kim, Hyeongsik, Koehler, Sebastian, Liener, Thomas, Long, Qinqin, Malone, James, McLaughlin, James A., McMurry, Julie A., Moxon, Sierra, Munoz-Torres, Monica C., Osumi-Sutherland, David, Overton, James A., Peters, Bjoern, Putman, Tim, Queralt-Rosinach, Núria, Shefchek, Kent, Solbrig, Harold, Thessen, Anne, Tudorache, Tania, Vasilevsky, Nicole, Wagner, Alex H., and Mungall, Christopher J.

Subjects
Computer Science - Databases
Abstract

Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Are they associated in some other way? Such relationships between the mapped terms are often not documented, leading to incorrect assumptions and making them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Also, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. The Simple Standard for Sharing Ontological Mappings (SSSOM) addresses these problems by: 1. Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. 2. Defining an easy to use table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data standards. 3. Implementing open and community-driven collaborative workflows designed to evolve the standard continuously to address changing requirements and mapping practices. 4. Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases, and survey some existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable, and Reusable (FAIR). The SSSOM specification is at http://w3id.org/sssom/spec., Comment: Corresponding author: Christopher J. Mungall

Published
2021
Full Text
View/download PDF

5. The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease

Author

Carmody, Leigh C., Gargano, Michael A., Toro, Sabrina, Vasilevsky, Nicole A., Adam, Margaret P., Blau, Hannah, Chan, Lauren E., Gomez-Andres, David, Horvath, Rita, Kraus, Megan L., Ladewig, Markus S., Lewis-Smith, David, Lochmüller, Hanns, Matentzoglu, Nicolas A., Munoz-Torres, Monica C., Schuetz, Catharina, Seitz, Berthold, Similuk, Morgan N., Sparks, Teresa N., Strauss, Timmy, Swietlik, Emilia M., Thompson, Rachel, Zhang, Xingmin Aaron, Mungall, Christopher J., Haendel, Melissa A., and Robinson, Peter N.

Published
2023
Full Text
View/download PDF

6. A quick guide for student-driven community genome annotation

Author

Hosmani, Prashant S., Shippy, Teresa, Miller, Sherry, Benoit, Joshua B., Munoz-Torres, Monica, Flores, Mirella, Mueller, Lukas A., Wiersma-Koch, Helen, D'elia, Tom, Brown, Susan J., and Saha, Surya

Subjects
Quantitative Biology - Genomics
Abstract

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification. Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for both education and improved genomic resources. We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators. This model can be scaled to large teams and includes quality control processes through incremental evaluation. Moreover, it gives students an opportunity to increase their understanding of genome biology and to participate in scientific research in collaboration with peers and senior researchers at multiple institutions.

Published
2018
Full Text
View/download PDF

7. GA4GH: International policies and standards for data sharing across genomic research and healthcare

Author

Rehm, Heidi L., Page, Angela J.H., Smith, Lindsay, Adams, Jeremy B., Alterovitz, Gil, Babb, Lawrence J., Barkley, Maxmillian P., Baudis, Michael, Beauvais, Michael J.S., Beck, Tim, Beckmann, Jacques S., Beltran, Sergi, Bernick, David, Bernier, Alexander, Bonfield, James K., Boughtwood, Tiffany F., Bourque, Guillaume, Bowers, Sarion R., Brookes, Anthony J., Brudno, Michael, Brush, Matthew H., Bujold, David, Burdett, Tony, Buske, Orion J., Cabili, Moran N., Cameron, Daniel L., Carroll, Robert J., Casas-Silva, Esmeralda, Chakravarty, Debyani, Chaudhari, Bimal P., Chen, Shu Hui, Cherry, J. Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L., Cook-Deegan, Robert M., Courtot, Mélanie, Cunningham, Fiona, Cupak, Miro, Davies, Robert M., Denisko, Danielle, Doerr, Megan J., Dolman, Lena I., Dove, Edward S., Dursi, L. Jonathan, Dyke, Stephanie O.M., Eddy, James A., Eilbeck, Karen, Ellrott, Kyle P., Fairley, Susan, Fakhro, Khalid A., Firth, Helen V., Fitzsimons, Michael S., Fiume, Marc, Flicek, Paul, Fore, Ian M., Freeberg, Mallory A., Freimuth, Robert R., Fromont, Lauren A., Fuerth, Jonathan, Gaff, Clara L., Gan, Weiniu, Ghanaim, Elena M., Glazer, David, Green, Robert C., Griffith, Malachi, Griffith, Obi L., Grossman, Robert L., Groza, Tudor, Guidry Auvil, Jaime M., Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A., Hamosh, Ada, Hansen, David P., Hart, Reece K., Hartley, Dean Mitchell, Haussler, David, Hendricks-Sturrup, Rachele M., Ho, Calvin W.L., Hobb, Ashley E., Hoffman, Michael M., Hofmann, Oliver M., Holub, Petr, Hsu, Jacob Shujui, Hubaux, Jean-Pierre, Hunt, Sarah E., Husami, Ammar, Jacobsen, Julius O., Jamuar, Saumya S., Janes, Elizabeth L., Jeanson, Francis, Jené, Aina, Johns, Amber L., Joly, Yann, Jones, Steven J.M., Kanitz, Alexander, Kato, Kazuto, Keane, Thomas M., Kekesi-Lafrance, Kristina, Kelleher, Jerome, Kerry, Giselle, Khor, Seik-Soon, Knoppers, Bartha M., Konopko, Melissa A., Kosaki, Kenjiro, Kuba, Martin, Lawson, Jonathan, Leinonen, Rasko, Li, Stephanie, Lin, Michael F., Linden, Mikael, Liu, Xianglin, Liyanage, Isuru Udara, Lopez, Javier, Lucassen, Anneke M., Lukowski, Michael, Mann, Alice L., Marshall, John, Mattioni, Michele, Metke-Jimenez, Alejandro, Middleton, Anna, Milne, Richard J., Molnár-Gábor, Fruzsina, Mulder, Nicola, Munoz-Torres, Monica C., Nag, Rishi, Nakagawa, Hidewaki, Nasir, Jamal, Navarro, Arcadi, Nelson, Tristan H., Niewielska, Ania, Nisselle, Amy, Niu, Jeffrey, Nyrönen, Tommi H., O’Connor, Brian D., Oesterle, Sabine, Ogishima, Soichi, Ota Wang, Vivian, Paglione, Laura A.D., Palumbo, Emilio, Parkinson, Helen E., Philippakis, Anthony A., Pizarro, Angel D., Prlic, Andreas, Rambla, Jordi, Rendon, Augusto, Rider, Renee A., Robinson, Peter N., Rodarmer, Kurt W., Rodriguez, Laura Lyman, Rubin, Alan F., Rueda, Manuel, Rushton, Gregory A., Ryan, Rosalyn S., Saunders, Gary I., Schuilenburg, Helen, Schwede, Torsten, Scollen, Serena, Senf, Alexander, Sheffield, Nathan C., Skantharajah, Neerjah, Smith, Albert V., Sofia, Heidi J., Spalding, Dylan, Spurdle, Amanda B., Stark, Zornitza, Stein, Lincoln D., Suematsu, Makoto, Tan, Patrick, Tedds, Jonathan A., Thomson, Alastair A., Thorogood, Adrian, Tickle, Timothy L., Tokunaga, Katsushi, Törnroos, Juha, Torrents, David, Upchurch, Sean, Valencia, Alfonso, Guimera, Roman Valls, Vamathevan, Jessica, Varma, Susheel, Vears, Danya F., Viner, Coby, Voisin, Craig, Wagner, Alex H., Wallace, Susan E., Walsh, Brian P., Williams, Marc S., Winkler, Eva C., Wold, Barbara J., Wood, Grant M., Woolley, J. Patrick, Yamasaki, Chisato, Yates, Andrew D., Yung, Christina K., Zass, Lyndon J., Zaytseva, Ksenia, Zhang, Junjun, Goodhand, Peter, North, Kathryn, and Birney, Ewan

Published
2021
Full Text
View/download PDF

9. The 2016 Bioinformatics Open Source Conference (BOSC).

Author

Harris, Nomi, Cock, Peter, Chapman, Brad, Fields, Christopher, Hokamp, Karsten, Lapp, Hilmar, Muñoz-Torres, Monica, and Wiencko, Heather

Subjects
Bioinformatics, open science, open source
Abstract

Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.

Published
2016

10. Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile)

Author

Smith, Christopher D., Zimin, Aleksey, Holt, Carson, Abouheif, Ehab, Benton, Richard, Cash, Elizabeth, Croset, Vincent, Currie, Cameron R., Elhaik, Eran, Elsik, Christine G., Fave, Marie-Julie, Fernandes, Vilaiwan, Gadau, Jürgen, Gibson, Joshua D., Graur, Dan, Grubbs, Kirk J., Hagen, Darren E., Helmkampf, Martin, Holley, Jo-Anne, Hu, Hao, Viniegra, Ana Sofia Ibarraran, Johnson, Brian R., Johnson, Reed M., Khila, Abderrahman, Kim, Jay W., Laird, Joseph, Mathis, Kaitlyn A., Moeller, Joseph A., Muñoz-Torres, Monica C., Murphy, Marguerite C., Nakamura, Rin, Nigam, Surabhi, Overson, Rick P., Placek, Jennifer E., Rajakumar, Rajendhran, Reese, Justin T., Robertson, Hugh M., Smith, Chris R., Suarez, Andrew V., Suen, Garret, Suhr, Elissa L., Tao, Shu, Torres, Candice W., van Wilgenburg, Ellen, Viljakainen, Lumi, Walden, Kimberly K. O., Wild, Alexander L., Yandell, Mark, Yorke, James A., Tsutsui, Neil D., and Robinson, Gene E.

Published
2011

11. Draft genome of the red harvester ant Pogonomyrmex barbatus

Author

Smith, Chris R., Smith, Christopher D., Robertson, Hugh M., Helmkampf, Martin, Zimin, Aleksey, Yandell, Mark, Holt, Carson, Hu, Hao, Abouheif, Ehab, Benton, Richard, Cash, Elizabeth, Croset, Vincent, Currie, Cameron R., Elhaik, Eran, Elsik, Christine G., Favé, Marie-Julie, Fernandes, Vilaiwan, Gibson, Joshua D., Graur, Dan, Gronenberg, Wulfila, Grubbs, Kirk J., Hagen, Darren E., Viniegra, Ana Sofia Ibarraran, Johnson, Brian R., Johnson, Reed M., Khila, Abderrahman, Kim, Jay W., Mathis, Kaitlyn A., Munoz-Torres, Monica C., Murphy, Marguerite C., Mustard, Julie A., Nakamura, Rin, Niehuis, Oliver, Nigam, Surabhi, Overson, Rick P., Placek, Jennifer E., Rajakumar, Rajendhran, Reese, Justin T., Suen, Garret, Tao, Shu, Torres, Candice W., Tsutsui, Neil D., Viljakainen, Lumi, Wolschin, Florian, Gadau, Jürgen, and Robinson, Gene E.

Published
2011

14. Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series

Author

Giraldo Martha C, Muñoz-Torres Monica C, Chavarro Carolina M, Hurtado Natalia, Blair Matthew W, Pedraza Fabio, Tomkins Jeff, and Wing Rod

Subjects
Botany, QK1-989
Abstract

Abstract Background Sequencing of cDNA libraries for the development of expressed sequence tags (ESTs) as well as for the discovery of simple sequence repeats (SSRs) has been a common method of developing microsatellites or SSR-based markers. In this research, our objective was to further sequence and develop common bean microsatellites from leaf and root cDNA libraries derived from the Andean gene pool accession G19833 and the Mesoamerican gene pool accession DOR364, mapping parents of a commonly used reference map. The root libraries were made from high and low phosphorus treated plants. Results A total of 3,123 EST sequences from leaf and root cDNA libraries were screened and used for direct simple sequence repeat discovery. From these EST sequences we found 184 microsatellites; the majority containing tri-nucleotide motifs, many of which were GC rich (ACC, AGC and AGG in particular). Di-nucleotide motif microsatellites were about half as common as the tri-nucleotide motif microsatellites but most of these were AGn microsatellites with a moderate number of ATn microsatellites in root ESTs followed by few ACn and no GCn microsatellites. Out of the 184 new SSR loci, 120 new microsatellite markers were developed in the BMc (Bean Microsatellites from cDNAs) series and these were evaluated for their capacity to distinguish bean diversity in a germplasm panel of 18 genotypes. We developed a database with images of the microsatellites and their polymorphism information content (PIC), which averaged 0.310 for polymorphic markers. Conclusions The present study produced information about microsatellite frequency in root and leaf tissues of two important genotypes for common bean genomics: namely G19833, the Andean genotype selected for whole genome shotgun sequencing from race Peru, and DOR364 a race Mesoamerica subgroup 2 genotype that is a small-red seeded, released variety in Central America. Both race Peru and Mesoamerica subgroup 2 (small red beans) have been understudied in comparison to race Nueva Granada and Mesoamerica subgroup 1 (black beans) both with regards to gene expression and as sources of markers. However, we found few differences between SSR type and frequency between the G19833 leaf and DOR364 root tissue-derived ESTs. Overall, our work adds to the analysis of microsatellite frequency evaluation for common bean and provides a new set of 120 BMc markers which combined with the 248 previously developed BMc markers brings the total in this series to 368 markers. Once we include BMd markers, which are derived from GenBank sequences, the current total of gene-based markers from our laboratory surpasses 500 markers. These markers are basic for studies of the transcriptome of common bean and can form anchor points for genetic mapping studies in the future.

Published
2011
Full Text
View/download PDF

15. The development and characterisation of a bacterial artificial chromosome library for Fragaria vesca

Author

Abbott Albert G, Monfort Amparo, Muñoz-Torres Monica C, Sargent Daniel J, Girona Elena, Bonet Julio, Arús Pere, Simpson David W, and Davik Jahn

Subjects
Medicine, Biology (General), QH301-705.5, Science (General), Q1-390
Abstract

Abstract Background The cultivated strawberry Fragaria ×ananassa is one of the most economically-important soft-fruit species. Few structural genomic resources have been reported for Fragaria and there exists an urgent need for the development of physical mapping resources for the genus. The first stage in the development of a physical map for Fragaria is the construction and characterisation of a high molecular weight bacterial artificial chromosome (BAC) library. Methods A BAC library, consisting of 18,432 clones was constructed from Fragaria vesca f. semperflorens accession 'Ali Baba'. BAC DNA from individual library clones was pooled to create a PCR-based screening assay for the library, whereby individual clones could be identified with just 34 PCR reactions. These pools were used to screen the BAC library and anchor individual clones to the diploid Fragaria reference map (FV×FN). Findings Clones from the BAC library developed contained an average insert size of 85 kb, representing over seven genome equivalents. The pools and superpools developed were used to identify a set of BAC clones containing 70 molecular markers previously mapped to the diploid Fragaria FV×FN reference map. The number of positive colonies identified for each marker suggests the library represents between 4× and 10× coverage of the diploid Fragaria genome, which is in accordance with the estimate of library coverage based on average insert size. Conclusion This BAC library will be used for the construction of a physical map for F. vesca and the superpools will permit physical anchoring of molecular markers using PCR.

Published
2009
Full Text
View/download PDF

16. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

Author

Ma, Sean, Chen, Yolanda, Ma, Martin, Benoit, Joshua, Bhandari, Anita, Bowsher, Julia, Brevik, Kristian, Cappelle, Kaat, Li, Mei-Ju, Childers, Anna, Li, Christopher, Christiaens, Olivier, Ma, Justin, Didion, Elise, Elpidina, Elena, Engsontia, Patamarerk, Ma, Markus, García-Robles, Inmaculada, Gibbs, Richard, Goswami, Chandan, Grapputo, Alessandro, Gruden, Kristina, Ma, Marcin, Ma, Bernard, Jennings, Emily, Jones, Jeffery, Kalsi, Megha, Khan, Sher, Kumar, Abhishek, Li, Fei, Ma, Vincent, Ma, Xingzhou, Martynov, Alex, Miller, Nicholas, Mitchell, Robert, Muñoz-Torres, Monica, Muszewska, Anna, Oppert, Brenda, Palli, Subba Reddy, Panfilio, Kristen, Pauchet, Yannick, Perkin, Lindsey, Petek, Marko, Poelchau, Monica, Record, Eric, Rinehart, Joseph, Robertson, Hugh, Rosendale, Andrew, Ruiz-Arroyo, Victor, Smagghe, Guy, Szendrei, Zsofia, Thomas, Gregg, Torson, Alex, Vargas Jentzsch, Iris, Weirauch, Matthew, Yates, Ashley, Yocum, George, Yoon, June-Sun, Richards, Stephen, Schoville, Sean, Andersson, Martin, Chen, Mei-Ju, Childers, Christopher, Clements, Justin, Friedrich, Markus, Grynberg, Marcin, Henrissat, Bernard, Lombard, Vincent, Ma, Alexander, Li, Lindsey, Ma, Marko, Robertson, Robert, Thomas, Gregg W.C., Ma, Matthew, Richards, Richard, Human Genome Sequencing Center [Houston] (HGSC), Baylor College of Medicine (BCM), Baylor University-Baylor University, Centre of Excellence in Biological interactions (CoE), University of Helsinki-Universität Zürich [Zürich] = University of Zurich (UZH)-University of Jyväskylä (JYU), National Institute of Biology, Max Planck Institute for Chemical Ecology, Max-Planck-Gesellschaft, Institut Pascal (IP), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-SIGMA Clermont (SIGMA Clermont)-Centre National de la Recherche Scientifique (CNRS), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Entomology, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Department of Biology, Georgetown University, Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)-École Centrale de Marseille (ECM), Faculty of Bioscience Engineering [Ghent], Universiteit Gent = Ghent University [Belgium] (UGENT), Indiana University [Bloomington], Indiana University System, Human Genome Sequencing Center, Institute of Modern Physics, Fudan University [Shanghai], Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), NIH NHGRI U54 HG003273 K12 GM000708, UVM Agricultural Experiment Station Hatch grant VT-H02010, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy DE-AC02-05CH11231, National Science Centre2012/07/D/NZ2/04286, NIH (NIGMS) 5R01GM080203, NIH (NHGRI)5R01HG004483, University of Helsinki-University of Zürich [Zürich] (UZH)-University of Jyväskylä, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Sigma CLERMONT (Sigma CLERMONT)-Centre National de la Recherche Scientifique (CNRS), École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Ghent University [Belgium] (UGENT), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Universität Zürich [Zürich] = University of Zurich (UZH)-University of Jyväskylä (JYU), Georgetown University [Washington] (GU), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), and Universiteit Gent = Ghent University (UGENT)

Subjects
Male, 0106 biological sciences, 0301 basic medicine, Genome, Insect, lcsh:Medicine, 01 natural sciences, Genome, Nucleotide diversity, Insecticide Resistance, pomme de terre, TRIBOLIUM-CASTANEUM, lcsh:Science, Leptinotarsa, CYSTEINE PROTEINASES, Phylogeny, 2. Zero hunger, education.field_of_study, Multidisciplinary, biology, insecte ravageur, Ecology, Genètica vegetal, Agriculture, leptinotarsa decemlineata, Genomics, S-TRANSFERASE GENES, lutte contre les ravageurs, Coleoptera, Other Physical Sciences, phénotype, espèce modèle, Multigene Family, Insect Proteins, RNA Interference, Female, Biotechnology, Autre (Sciences du Vivant), Genome evolution, doryphore, coleoptera, Evolution, Population, RNA-INTERFERENCE, GEOGRAPHIC POPULATIONS, Article, DNA sequencing, Host-Parasite Interactions, Evolution, Molecular, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Animals, analyse génomique, Pest Control, Biological, education, QH426, Gene, Solanum tuberosum, Comparative genomics, business.industry, chrysomelidae, lcsh:R, Human Genome, fungi, Colorado potato beetle, Pest control, Biology and Life Sciences, Molecular, Genetic Variation, Molecular Sequence Annotation, Biological, biology.organism_classification, 010602 entomology, Genòmica, Genetics, Population, 030104 developmental biology, Gene Expression Regulation, DROSOPHILA-MELANOGASTER, PROTEINASE-INHIBITORS, Evolutionary biology, TRANSPOSABLE ELEMENTS, DNA Transposable Elements, lcsh:Q, Pest Control, Biochemistry and Cell Biology, PEST analysis, CAENORHABDITIS-ELEGANS, business, Insect, Transcription Factors
Abstract

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.

Published
2017
Full Text
View/download PDF

17. Colombia's cyberinfrastructure for biodiversity: Building data infrastructure in emerging countries to foster socioeconomic growth.

Author

De Vega, Jose J., Davey, Robert P., Duitama, Jorge, Escobar, Dairo, Cristancho‐Ardila, Marco A., Etherington, Graham J., Minotto, Alice, Arenas‐Suarez, Nelson E., Pineda‐Cardenas, Juan D., Correa‐Alvarez, Javier, Camargo Rodriguez, Anyela V., Haerty, Wilfried, Mallarino‐Robayo, Juan P., Barreto‐Hernandez, Emiliano, Muñoz‐Torres, Monica, Fernandez‐Fuentes, Narcis, and Di Palma, Federica

Subjects
CYBERINFRASTRUCTURE, BIODIVERSITY, SOCIOECONOMICS, ELECTRONIC information resources, DIGITAL technology
Abstract

Societal Impact Statement: Colombia is a "megadiverse" country with vast natural resources. A history of recent conflict means that information is only now being collected on the natural capital of regions that were previously unexplored. Better access to data, tools, and expertise is required for evidence‐supported decisions on the conservation of these resources. The development of a bespoke cyberinfrastructure could help fulfill this need by providing access to digital resources in a collaborative cyberenvironment. We outline key priorities and develop a reference framework for building cyberinfrastructure in Colombia. This framework could be applied to other fields and countries to promote knowledge exchange, scientific innovation, and socioeconomic growth. [ABSTRACT FROM AUTHOR]

Published
2020
Full Text
View/download PDF

18. The i5K Initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment

Author

Evans, Jay D., Brown, Susan J., Hackett, Kevin J., Robinson, Gene, Richards, Stephen, Lawson, Daniel, Elsik, Christine, Coddington, Jonathan, Edwards, Owain, Emrich, Scott, Gabaldon, Toni, Goldsmith, Marian, Hanes, Glenn, Misof, Bernhard, Muñoz-Torres, Monica, Niehuis, Oliver, Papanicolaou, Alexis, Pfrender, Michael, Poelchau, Monica, Purcell-Miramontes, Mary, Robertson, Hugh M., Ryder, Oliver, Tagu, Denis, Torres, Tatiana, Zdobnov, Evgeny, Zhang, Guojie, Zhou, Xin, i5K Consortium, Agricultural Research Service (ARS), United States Department of Agriculture, Kansas State University, University of Illinois System, Human Genome Sequencing Center, Baylor College of Medicine (BCM), Baylor University-Baylor University, European Bioinformatics Institute, University of Missouri [Columbia], University of Missouri System, Smithsonian Institution National Museum of Natural History (NMNH), Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), University of Notre Dame [Indiana] (UND), Centre for Genomic Regulation (CRG), University of Rhode Island (URI), Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Genomics Division [LBNL Berkeley], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Ecosystem Sciences, Department of Biology, Georgetown University, National Institute of Food and Agriculture, San Diego Zoo's Institute for Conservation Research, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, University of São Paulo, Medical School, Université de Genève (UNIGE), Beijing Genomics Institute, American Genetic Association, the Arthropod Genomics Center (Kansas State University), and the US Department of Agriculture (National Institute for Food and Agriculture and Agricultural Research Service), USDA-ARS : Agricultural Research Service, University of Missouri [Columbia] (Mizzou), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Beijing Genomics Institute [Shenzhen] (BGI), Georgetown University [Washington] (GU), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Genève = University of Geneva (UNIGE), and Zdobnov, Evgeny

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], agriculture, comparative genomics, insect evolution, disease vector, genome sequencing, Biodiversity, Genomics, GENOMAS, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Human health, Genetics, Animals, ddc:576.5, Marine ecosystem, Arthropods, Molecular Biology, Genetics (clinical), 030304 developmental biology, Comparative genomics, 0303 health sciences, biology, business.industry, Ecology, Environmental resource management, Chromosome Mapping, Arthropods/genetics, biology.organism_classification, Agriculture, Informatics, Perspective, Arthropod, business, Biotechnology
Abstract

International audience; Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world's terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists, With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind.

Published
2013
Full Text
View/download PDF

19. The 2016 Bioinformatics Open Source Conference (BOSC)

Author

Harris, Nomi L., primary, Cock, Peter J.A., additional, Chapman, Brad, additional, Fields, Christopher J., additional, Hokamp, Karsten, additional, Lapp, Hilmar, additional, Muñoz-Torres, Monica, additional, and Wiencko, Heather, additional

Published
2016
Full Text
View/download PDF

20. Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality

Author

Simola, Daniel F., Wissler, Lothar, Donahue, Greg, Waterhouse, Robert M., Helmkampf, Martin, Roux, Julien, Nygaard, Sanne, Glastad, Karl M., Hagen, Darren E., Viljakainen, Lumi, Reese, Justin T, Hunt, Brendan G, Graur, Dan, Elhaik, Eran, Kriventseva, Evgenia V, Wen, Jiayu, Parker, Brian John, Cash, Elizabeth, Privman, Eyal, Childers, Christopher P, Muñoz-Torres, Monica C, Boomsma, Jacobus Jan, Bornberg-Bauer, Erich, Currie, Cameron R, Elsik, Christine G, Suen, Garret, Goodisman, Michael A D, Keller, Laurent, Liebig, Jürgen, Rawls, Alan, Reinberg, Danny, Smith, Chris D, Smith, Chris R, Tsutsui, Neil, Wurm, Yannick, Zdobnov, Evgeny M, Berger, Shelley L, Gadau, Jürgen, Simola, Daniel F., Wissler, Lothar, Donahue, Greg, Waterhouse, Robert M., Helmkampf, Martin, Roux, Julien, Nygaard, Sanne, Glastad, Karl M., Hagen, Darren E., Viljakainen, Lumi, Reese, Justin T, Hunt, Brendan G, Graur, Dan, Elhaik, Eran, Kriventseva, Evgenia V, Wen, Jiayu, Parker, Brian John, Cash, Elizabeth, Privman, Eyal, Childers, Christopher P, Muñoz-Torres, Monica C, Boomsma, Jacobus Jan, Bornberg-Bauer, Erich, Currie, Cameron R, Elsik, Christine G, Suen, Garret, Goodisman, Michael A D, Keller, Laurent, Liebig, Jürgen, Rawls, Alan, Reinberg, Danny, Smith, Chris D, Smith, Chris R, Tsutsui, Neil, Wurm, Yannick, Zdobnov, Evgeny M, Berger, Shelley L, and Gadau, Jürgen

Abstract

Genomes of eusocial insects code for dramatic examples of phenotypic plasticity and social organization. We compared the genomes of seven ants, the honeybee, and various solitary insects to examine whether eusocial lineages share distinct features of genomic organization. Each ant lineage contains ∼4000 novel genes, but only 64 of these genes are conserved among all seven ants. Many gene families have been expanded in ants, notably those involved in chemical communication (e.g., desaturases and odorant receptors). Alignment of the ant genomes revealed reduced purifying selection compared with Drosophila without significantly reduced synteny. Correspondingly, ant genomes exhibit dramatic divergence of noncoding regulatory elements; however, extant conserved regions are enriched for novel noncoding RNAs and transcription factor-binding sites. Comparison of orthologous gene promoters between eusocial and solitary species revealed significant regulatory evolution in both cis (e.g., Creb) and trans (e.g., fork head) for nearly 2000 genes, many of which exhibit phenotypic plasticity. Our results emphasize that genomic changes can occur remarkably fast in ants, because two recently diverged leaf-cutter ant species exhibit faster accumulation of species-specific genes and greater divergence in regulatory elements compared with other ants or Drosophila. Thus, while the "socio-genomes" of ants and the honeybee are broadly characterized by a pervasive pattern of divergence in gene composition and regulation, they preserve lineage-specific regulatory features linked to eusociality. We propose that changes in gene regulation played a key role in the origins of insect eusociality, whereas changes in gene composition were more relevant for lineage-specific eusocial adaptations.

Published
2013

21. Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality

Author

Simola, Daniel F., primary, Wissler, Lothar, additional, Donahue, Greg, additional, Waterhouse, Robert M., additional, Helmkampf, Martin, additional, Roux, Julien, additional, Nygaard, Sanne, additional, Glastad, Karl M., additional, Hagen, Darren E., additional, Viljakainen, Lumi, additional, Reese, Justin T., additional, Hunt, Brendan G., additional, Graur, Dan, additional, Elhaik, Eran, additional, Kriventseva, Evgenia V., additional, Wen, Jiayu, additional, Parker, Brian J., additional, Cash, Elizabeth, additional, Privman, Eyal, additional, Childers, Christopher P., additional, Muñoz-Torres, Monica C., additional, Boomsma, Jacobus J., additional, Bornberg-Bauer, Erich, additional, Currie, Cameron R., additional, Elsik, Christine G., additional, Suen, Garret, additional, Goodisman, Michael A.D., additional, Keller, Laurent, additional, Liebig, Jürgen, additional, Rawls, Alan, additional, Reinberg, Danny, additional, Smith, Chris D., additional, Smith, Chris R., additional, Tsutsui, Neil, additional, Wurm, Yannick, additional, Zdobnov, Evgeny M., additional, Berger, Shelley L., additional, and Gadau, Jürgen, additional

Published
2013
Full Text
View/download PDF

25. Non-Coding Changes Cause Sex-Specific Wing Size Differences between Closely Related Species of Nasonia

Author

Loehlin, David W., primary, Oliveira, Deodoro C. S. G., additional, Edwards, Rachel, additional, Giebel, Jonathan D., additional, Clark, Michael E., additional, Cattani, M. Victoria, additional, van de Zande, Louis, additional, Verhulst, Eveline C., additional, Beukeboom, Leo W., additional, Muñoz-Torres, Monica, additional, and Werren, John H., additional

Published
2010
Full Text
View/download PDF

27. Whole genome analysis of a schistosomiasis-transmitting freshwater snail

Author

Adema, Coen M., Hillier, LaDeana W., Jones, Catherine S., Loker, Eric S., Knight, Matty, Minx, Patrick, Oliveira, Guilherme, Raghavan, Nithya, Shedlock, Andrew, do Amaral, Laurence Rodrigues, Arican-Goktas, Halime D., Assis, Juliana G., Baba, Elio Hideo, Baron, Olga L., Bayne, Christopher J., Bickham-Wright, Utibe, Biggar, Kyle K., Blouin, Michael, Bonning, Bryony C., Botka, Chris, Bridger, Joanna M., Buckley, Katherine M., Buddenborg, Sarah K., Lima Caldeira, Roberta, Carleton, Julia, Carvalho, Omar S., Castillo, Maria G., Chalmers, Iain W., Christensens, Mikkel, Clifton, Sandra, Cosseau, Celine, Coustau, Christine, Cripps, Richard M., Cuesta-Astroz, Yesid, Cummins, Scott F., di Stephano, Leon, Dinguirard, Nathalie, Duval, David, Emrich, Scott, Feschotte, Cédric, Feyereisen, Rene, FitzGerald, Peter, Fronick, Catrina, Fulton, Lucinda, Galinier, Richard, Gava, Sandra G., Geusz, Michael, Geyer, Kathrin K., Giraldo-Calderón, Gloria I., de Souza Gomes, Matheus, Gordy, Michelle A., Gourbal, Benjamin, Grunau, Christoph, Hanington, Patrick C., Hoffmann, Karl F., Hughes, Daniel, Humphries, Judith, Jackson, Daniel J., Jannotti-Passos, Liana K., de Jesus Jeremias, Wander, Jobling, Susan, Kamel, Bishoy, Kapusta, Aurélie, Kaur, Satwant, Koene, Joris M., Kohn, Andrea B., Lawson, Dan, Lawton, Scott P, Liang, Di, Limpanont, Yanin, Liu, Sijun, Lockyer, Anne E., Lovato, TyAnna L., Ludolf, Fernanda, Magrini, Vince, McManus, Donald P., Medina, Monica, Misra, Milind, Mitta, Guillaume, Mkoji, Gerald M., Montague, Michael J., Montelongo, Cesar, Moroz, Leonid L., Munoz-Torres, Monica C., Niazi, Umar, Noble, Leslie R., Oliveira, Francislon S., Pais, Fabiano S., Papenfuss, Anthony T., Peace, Rob, Pena, Janeth J., Pila, Emmanuel A., Quelais, Titouan, Raney, Brian J., Rast, Jonathan P., Rollinson, David, Rosse, Izinara C., Rotgans, Bronwyn, Routledge, Edwin J., Ryan, Kathryn M., Scholte, Larissa L. S., Storey, Kenneth B., Swain, Martin, Tennessen, Jacob A., Tomlinson, Chad, Trujillo, Damian L., Volpi, Emanuela V., Walker, Anthony J., Wang, Tianfang, Wannaporn, Ittiprasert, Warren, Wesley C., Wu, Xiao-Jun, Yoshino, Timothy P., Yusuf, Mohammed, Zhang, Si-Ming, Zhao, Min, and Wilson, Richard K.

Abstract

Biomphalaria snails are instrumental in transmission of the human blood fluke Schistosoma mansoni. With the World Health Organization's goal to eliminate schistosomiasis as a global health problem by 2025, there is now renewed emphasis on snail control. Here, we characterize the genome of Biomphalaria glabrata, a lophotrochozoan protostome, and provide timely and important information on snail biology. We describe aspects of phero-perception, stress responses, immune function and regulation of gene expression that support the persistence of B. glabrata in the field and may define this species as a suitable snail host for S. mansoni. We identify several potential targets for developing novel control measures aimed at reducing snail-mediated transmission of schistosomiasis.

Published
2017
Full Text
View/download PDF

28. The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions

Author

Engel, Philipp, Kwong, Waldan K., McFrederick, Quinn, Anderson, Kirk E., Barribeau, Seth Michael, Chandler, James Angus, Cornman, R. Scott, Dainat, Jacques, de Miranda, Joachim R., Doublet, Vincent, Emery, Olivier, Evans, Jay D., Farinelli, Laurent, Flenniken, Michelle L., Granberg, Fredrik, Grasis, Juris A., Gauthier, Laurent, Hayer, Juliette, Koch, Hauke, Kocher, Sarah, Martinson, Vincent G., Moran, Nancy, Munoz-Torres, Monica, Newton, Irene, Paxton, Robert J., Powell, Eli, Sadd, Ben M., Schmid-Hempel, Paul, Schmid-Hempel, Regula, Song, Se Jin, Schwarz, Ryan S., vanEngelsdorp, Dennis, and Dainat, Benjamin

Abstract

As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health.

Published
2016
Full Text
View/download PDF

29. The 2015 Bioinformatics Open Source Conference (BOSC 2015)

Author

Harris, Nomi L., Cock, Peter J. A., Lapp, Hilmar, Chapman, Brad, Davey, Rob, Fields, Christopher, Hokamp, Karsten, and Munoz-Torres, Monica

Subjects
Database and Informatics Methods, Bioinformatics, Computer and Information Sciences, Computer Software, Open Source Software, Science Policy, Open Science, Software Engineering, Software Development, Engineering and Technology, Reproducibility, Biology and Life Sciences, Organisms, Animals, Vertebrates, Birds, Zoology, Animal Anatomy, Feathers
Abstract

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included “Data Science;” “Standards and Interoperability;” “Open Science and Reproducibility;” “Translational Bioinformatics;” “Visualization;” and “Bioinformatics Open Source Project Updates”. In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled “Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community,” that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

Published
2016
Full Text
View/download PDF

30. Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes.

Author

Dunning Hotopp, Julie C., Clark, Michael E., Oliveira, Deodoro C. S. G., Foster, Jeremy M., Fischer, Peter, Muñoz Torres, Monica C., Giebel, Jonathan D., Kumar, Nikhil, Ishmael, Nadeeza, Shiliang Wang, Ingram, Jessica, Nene, Rahul V., Shepard, Jessica, Tomkins, Jeffrey, Richards, Stephen, Spiro, David J., Ghedin, Elodie, Slatko, Barton E., Tettelin, Hervé, and Werren, John H.

Subjects
*GENETIC transformation, *INTRACELLULAR pathogens, *EUKARYOTIC cells, *ENDOSYMBIOSIS, *GERM cells, *GENOMES, *NEMATODES, *WOLBACHIA, *PROKARYOTES
Abstract

Although common among bacteria, lateral gene transfer-the movement of genes between distantly related organisms-is thought to occur only rarely between bacteria and multicellular eukaryotes. However, the presence of endosymbionts, such as Wolbachia pipientis, within some eukaryotic germlines may facilitate bacterial gene transfers to eukaryotic host genomes. We therefore examined host genomes for evidence of gene transfer events from Wolbachia bacteria to their hosts. We found and confirmed transfers into the genomes of four insect and four nematode species that range from nearly the entire Wolbachia genome (>1 megabase) to short (<500 base pairs) insertions. Potential Wolbachia-to-host transfers were also detected computationally in three additional sequenced insect genomes. We also show that some of these inserted Wolbachia genes are transcribed within eukaryotic cells lacking endosymbionts. Therefore, heritable lateral gene transfer occurs into eukaryotic hosts from their prokaryote symbionts, potentially providing a mechanism for acquisition of new genes and functions. [ABSTRACT FROM AUTHOR]

Published
2007
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results