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2. Making Common Fund data more findable: catalyzing a data ecosystem

Author

Charbonneau, Amanda L, Brady, Arthur, Czajkowski, Karl, Aluvathingal, Jain, Canchi, Saranya, Carter, Robert, Chard, Kyle, Clarke, Daniel JB, Crabtree, Jonathan, Creasy, Heather H, D'Arcy, Mike, Felix, Victor, Giglio, Michelle, Gingrich, Alicia, Harris, Rayna M, Hodges, Theresa K, Ifeonu, Olukemi, Jeon, Minji, Kropiwnicki, Eryk, Lim, Marisa CW, Liming, R Lee, Lumian, Jessica, Mahurkar, Anup A, Mandal, Meisha, Munro, James B, Nadendla, Suvarna, Richter, Rudyard, Romano, Cia, Rocca-Serra, Philippe, Schor, Michael, Schuler, Robert E, Tangmunarunkit, Hongsuda, Waldrop, Alex, Williams, Cris, Word, Karen, Sansone, Susanna-Assunta, Ma'ayan, Avi, Wagner, Rick, Foster, Ian, Kesselman, Carl, Brown, C Titus, and White, Owen

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Good Health and Well Being, Ecosystem, Metadata, Financial Management
Abstract

The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables researchers to discover datasets from across the US National Institutes of Health Common Fund without requiring that data owners move, reformat, or rehost those data. This system is centered on a catalog that integrates detailed descriptions of biomedical datasets from individual Common Fund Programs' Data Coordination Centers (DCCs) into a uniform metadata model that can then be indexed and searched from a centralized portal. This Crosscut Metadata Model (C2M2) supports the wide variety of data types and metadata terms used by individual DCCs and can readily describe nearly all forms of biomedical research data. We detail its use to ingest and index data from 11 DCCs.

Published
2022

11. The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem

Author

Baron, J Allen, primary, Johnson, Claudia Sanchez-Beato, additional, Schor, Michael A, additional, Olley, Dustin, additional, Nickel, Lance, additional, Felix, Victor, additional, Munro, James B, additional, Bello, Susan M, additional, Bearer, Cynthia, additional, Lichenstein, Richard, additional, Bisordi, Katharine, additional, Koka, Rima, additional, Greene, Carol, additional, and Schriml, Lynn M, additional

Published
2023
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13. Discovery of a novel species, Theileria haneyi n. sp., infective to equids, highlights exceptional genomic diversity within the genus Theileria: implications for apicomplexan parasite surveillance

Author

Knowles, Donald P., Kappmeyer, Lowell S., Haney, Darrell, Herndon, David R., Fry, Lindsay M., Munro, James B., Sears, Kelly, Ueti, Massaro W., Wise, Lauren N., Silva, Marta, Schneider, David A., Grause, Juanita, White, Stephen N., Tretina, Kyle, Bishop, Richard P., Odongo, David O., Pelzel-McCluskey, Angela M., Scoles, Glen A., Mealey, Robert H., and Silva, Joana C.

Published
2018
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14. Associating HIV-1 envelope glycoprotein structures with states on the virus observed by smFRET

Author

Lu, Maolin, Ma, Xiaochu, Castillo-Menendez, Luis R., Gorman, Jason, Alsahafi, Nirmin, Ermel, Utz, Terry, Daniel S., Chambers, Michael, Peng, Dongjun, Zhang, Baoshan, Zhou, Tongqing, Reichard, Nick, Wang, Kevin, Grover, Jonathan R., Carman, Brennan P., Gardner, Matthew R., Nikić-Spiegel, Ivana, Sugawara, Akihiro, Arthos, James, Lemke, Edward A., Smith, III, Amos B., Farzan, Michael, Abrams, Cameron, Munro, James B., McDermott, Adrian B., Finzi, Andrés, Kwong, Peter D., Blanchard, Scott C., Sodroski, Joseph G., and Mothes, Walther

Published
2019
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15. Immunogenomic profile at baseline predicts host susceptibility to clinical malaria

Author

Mbambo, Gillian, primary, Dwivedi, Ankit, additional, Ifeonu, Olukemi O., additional, Munro, James B., additional, Shrestha, Biraj, additional, Bromley, Robin E., additional, Hodges, Theresa, additional, Adkins, Ricky S., additional, Kouriba, Bourema, additional, Diarra, Issa, additional, Niangaly, Amadou, additional, Kone, Abdoulaye K., additional, Coulibaly, Drissa, additional, Traore, Karim, additional, Dolo, Amagana, additional, Thera, Mahamadou A., additional, Laurens, Matthew B., additional, Doumbo, Ogobara K., additional, Plowe, Christopher V., additional, Berry, Andrea A., additional, Travassos, Mark, additional, Lyke, Kirsten E., additional, and Silva, Joana C., additional

Published
2023
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17. Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

Author

Moser, Kara A., Drábek, Elliott F., Dwivedi, Ankit, Stucke, Emily M., Crabtree, Jonathan, Dara, Antoine, Shah, Zalak, Adams, Matthew, Li, Tao, Rodrigues, Priscila T., Koren, Sergey, Phillippy, Adam M., Munro, James B., Ouattara, Amed, Sparklin, Benjamin C., Dunning Hotopp, Julie C., Lyke, Kirsten E., Sadzewicz, Lisa, Tallon, Luke J., Spring, Michele D., Jongsakul, Krisada, Lon, Chanthap, Saunders, David L., Ferreira, Marcelo U., Nyunt, Myaing M., Laufer, Miriam K., Travassos, Mark A., Sauerwein, Robert W., Takala-Harrison, Shannon, Fraser, Claire M., Sim, B. Kim Lee, Hoffman, Stephen L., Plowe, Christopher V., and Silva, Joana C.

Published
2020
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21. S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness

Author

Yurkovetskiy, Leonid, primary, Egri, Shawn, additional, Kurhade, Chaitanya, additional, Diaz-Salinas, Marco A., additional, Jaimes, Javier A., additional, Nyalile, Thomas, additional, Xie, Xuping, additional, Choudhary, Manish C., additional, Dauphin, Ann, additional, Li, Jonathan Z., additional, Munro, James B., additional, Shi, Pei-Yong, additional, Shen, Kuang, additional, and Luban, Jeremy, additional

Published
2023
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32. Making Common Fund data more findable: catalyzing a data ecosystem

Author

Charbonneau, Amanda L, primary, Brady, Arthur, additional, Czajkowski, Karl, additional, Aluvathingal, Jain, additional, Canchi, Saranya, additional, Carter, Robert, additional, Chard, Kyle, additional, Clarke, Daniel J B, additional, Crabtree, Jonathan, additional, Creasy, Heather H, additional, D'Arcy, Mike, additional, Felix, Victor, additional, Giglio, Michelle, additional, Gingrich, Alicia, additional, Harris, Rayna M, additional, Hodges, Theresa K, additional, Ifeonu, Olukemi, additional, Jeon, Minji, additional, Kropiwnicki, Eryk, additional, Lim, Marisa C W, additional, Liming, R Lee, additional, Lumian, Jessica, additional, Mahurkar, Anup A, additional, Mandal, Meisha, additional, Munro, James B, additional, Nadendla, Suvarna, additional, Richter, Rudyard, additional, Romano, Cia, additional, Rocca-Serra, Philippe, additional, Schor, Michael, additional, Schuler, Robert E, additional, Tangmunarunkit, Hongsuda, additional, Waldrop, Alex, additional, Williams, Cris, additional, Word, Karen, additional, Sansone, Susanna-Assunta, additional, Ma'ayan, Avi, additional, Wagner, Rick, additional, Foster, Ian, additional, Kesselman, Carl, additional, Brown, C Titus, additional, and White, Owen, additional

Published
2022
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33. Structure and immune recognition of trimeric pre-fusion HIV-1 Env

Author

Pancera, Marie, Zhou, Tongqing, Druz, Aliaksandr, Georgiev, Ivelin S., Soto, Cinque, Gorman, Jason, Huang, Jinghe, Acharya, Priyamvada, Chuang, Gwo-Yu, Ofek, Gilad, Stewart-Jones, Guillaume B.E., Stuckey, Jonathan, Bailer, Robert T., Joyce, M. Gordon, Louder, Mark K., Tumba, Nancy, Yang, Yongping, Zhang, Baoshan, Cohen, Myron S., Haynes, Barton F., Mascola, John R., Morris, Lynn, Munro, James B., Blanchard, Scott C., Mothes, Walther, Connors, Mark, and Kwong, Peter D.

Subjects
HIV antibodies -- Physiological aspects, Viral proteins -- Structure -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The human immunodeficiency virus type 1 (HIV-1) envelope (Env) spike, comprising three gp120 and three gp41 sub-units, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a post-fusion state. As the sole viral antigen on the HIV-1 virion surface, Env is both the target of neutralizing antibodies and a focus of vaccine efforts. Here we report the structure at 3.5 A resolution for an HIV-1 Env trimer captured in a mature closed state by antibodies PGT122 and 35O22. This structure reveals the prefusion conformation of gp41, indicates rearrangements needed for fusion activation, and defines parameters of immune evasion and immune recognition. Pre-fusion gp41 encircles amino- and carboxy- terminal strands of gp120 with four helices that form a membrane-proximal collar, fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry involve opening the clasp and expelling the termini. N-linked glycosylation and sequence- variable regions cover the pre-fusion closed spike; we used chronic cohorts to map the prevalence and location of effective HIV-1-neutralizing responses, which were distinguished by their recognition of N-linked glycan and tolerance for epitope-sequence variation., Over the last 50 years, more than 70 million people have been infected or killed by the human immunodeficiency virus type 1 (HIV-1) (1). A dominant contributing factor has been [...]

Published
2014
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34. The Human Disease Ontology 2022 update

Author

Schriml, Lynn M, primary, Munro, James B, additional, Schor, Mike, additional, Olley, Dustin, additional, McCracken, Carrie, additional, Felix, Victor, additional, Baron, J Allen, additional, Jackson, Rebecca, additional, Bello, Susan M, additional, Bearer, Cynthia, additional, Lichenstein, Richard, additional, Bisordi, Katharine, additional, Dialo, Nicole Campion, additional, Giglio, Michelle, additional, and Greene, Carol, additional

Published
2021
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35. Making Common Fund data more findable: Catalyzing a Data Ecosystem

Author

Charbonneau, Amanda L, primary, Brady, Arthur, additional, Czajkowski, Karl, additional, Aluvathingal, Jain, additional, Canchi, Saranya, additional, Carter, Robert, additional, Chard, Kyle, additional, Clarke, Daniel J.B., additional, Creasy, Heather H, additional, D’Arcy, Mike, additional, Giglio, Michelle, additional, Gingrich, Alicia, additional, Harris, Rayna M, additional, Hodges, Theresa K, additional, Ifeonu, Olukemi, additional, Jeon, Minji, additional, Kropiwnicki, Eryk, additional, Lim, Marisa C.W., additional, Liming, R. Lee, additional, Mandal, Meisha, additional, Munro, James B, additional, Nadendla, Suvarna, additional, Richter, Rudyard, additional, Romano, Cia, additional, Rocca-Serra, Philippe, additional, Schuler, Robert E., additional, Tangmunarunkit, Hongsuda, additional, Waldrop, Alex, additional, Williams, Cris, additional, Word, Karen, additional, Sansone, Susanna-Assunta, additional, Ma’ayan, Avi, additional, Wagner, Rick, additional, Foster, Ian, additional, Kesselman, Carl, additional, Brown, C. Titus, additional, and White, Owen, additional

Published
2021
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39. ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts

Author

Hobbs, Elizabeth T., primary, Goralski, Stephen M., additional, Mitchell, Ashley, additional, Simpson, Andrew, additional, Leka, Dorjan, additional, Kotey, Emmanuel, additional, Sekira, Matt, additional, Munro, James B., additional, Nadendla, Suvarna, additional, Jackson, Rebecca, additional, Gonzalez-Aguirre, Aitor, additional, Krallinger, Martin, additional, Giglio, Michelle, additional, and Erill, Ivan, additional

Published
2021
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40. A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopy

Author

McGovern Institute for Brain Research at MIT, Program in Media Arts and Sciences (Massachusetts Institute of Technology), Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Neurobiological Engineering, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Gao, Ruixuan, Yu, Chih-Chieh, Gao, Linyi, Piatkevich, Kiryl D, Neve, Rachael L, Munro, James B, Upadhyayula, Srigokul, Boyden, Edward S, McGovern Institute for Brain Research at MIT, Program in Media Arts and Sciences (Massachusetts Institute of Technology), Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Center for Neurobiological Engineering, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Gao, Ruixuan, Yu, Chih-Chieh, Gao, Linyi, Piatkevich, Kiryl D, Neve, Rachael L, Munro, James B, Upadhyayula, Srigokul, and Boyden, Edward S

Abstract

Expansion microscopy (ExM) physically magnifies biological specimens to enable nanoscale-resolution imaging using conventional microscopes. Current ExM methods permeate specimens with free-radical-chain-growth-polymerized polyacrylate hydrogels, whose network structure limits the local isotropy of expansion as well as the preservation of morphology and shape at the nanoscale. Here we report that ExM is possible using hydrogels that have a more homogeneous network structure, assembled via non-radical terminal linking of tetrahedral monomers. As with earlier forms of ExM, such 'tetra-gel'-embedded specimens can be iteratively expanded for greater physical magnification. Iterative tetra-gel expansion of herpes simplex virus type 1 (HSV-1) virions by ~10× in linear dimension results in a median spatial error of 9.2 nm for localizing the viral envelope layer, rather than 14.3 nm from earlier versions of ExM. Moreover, tetra-gel-based expansion better preserves the virion spherical shape. Thus, tetra-gels may support ExM with reduced spatial errors and improved local isotropy, pointing the way towards single-biomolecule accuracy ExM.

Published
2021

41. ECO-CollecTF: A corpus of annotated evidence-based assertions in biomedical manuscripts

Author

Barcelona Supercomputing Center, Hobbs, Elizabeth T., Goralski, Stephen M., Mitchell, Ashley, Simpson, Andrew, Leka, Dorjan, Kotey, Emmanuel, Sekira, Matt, Munro, James B., Nadendla, Suvarna, Jackson, Rebecca, Gonzalez Aguirre, Aitor, Krallinger, Martin, Giglio, Michelle, Erill, Ivan, Barcelona Supercomputing Center, Hobbs, Elizabeth T., Goralski, Stephen M., Mitchell, Ashley, Simpson, Andrew, Leka, Dorjan, Kotey, Emmanuel, Sekira, Matt, Munro, James B., Nadendla, Suvarna, Jackson, Rebecca, Gonzalez Aguirre, Aitor, Krallinger, Martin, Giglio, Michelle, and Erill, Ivan

Abstract

Analysis of high-throughput experiments in the life sciences frequently relies upon standardized information about genes, gene products, and other biological entities. To provide this information, expert curators are increasingly relying on text mining tools to identify, extract and harmonize statements from biomedical journal articles that discuss findings of interest. For determining reliability of the statements, curators need the evidence used by the authors to support their assertions. It is important to annotate the evidence directly used by authors to qualify their findings rather than simply annotating mentions of experimental methods without the context of what findings they support. Text mining tools require tuning and adaptation to achieve accurate performance. Many annotated corpora exist to enable developing and tuning text mining tools; however, none currently provides annotations of evidence based on the extensive and widely used Evidence and Conclusion Ontology. We present the ECO-CollecTF corpus, a novel, freely available, biomedical corpus of 84 documents that captures high-quality, evidence-based statements annotated with the Evidence and Conclusion Ontology., This work was supported by the National Science Foundation, Division of Biological Infrastructure (1458400) and the National Institutes of Health (R01GM089636, U41HG008735), and by a management commission from Plan TL (Plan de Impulso de las Tecnologías del Lenguaje) of the Spanish Ministerio de Asuntos Económicos y Transformación Digital to BSC-CNS., Peer Reviewed, Postprint (published version)

Published
2021

44. Navigating the ribosome's metastable energy landscape

Author

Munro, James B., Sanbonmatsu, Kevin Y., Spahn, Christian M.T., and Blanchard, Scott C.

Subjects
Proteins -- Physiological aspects, Transfer RNA -- Physiological aspects, Biological sciences, Chemistry
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.tibs.2009.04.004 Byline: James B. Munro (1), Kevin Y. Sanbonmatsu (2), Christian M.T. Spahn (3), Scott C. Blanchard (1) Abstract: The molecular mechanisms by which tRNA molecules enter and transit the ribosome during mRNA translation remains elusive. However, recent genetic, biochemical and structural studies offer important new findings into the ordered sequence of events underpinning the translocation process that help place the molecular mechanism within reach. In particular, new structural and kinetic insights have been obtained regarding tRNA movements through 'hybrid state' configurations. These dynamic views reveal that the macromolecular ribosome particle, like many smaller proteins, has an intrinsic capacity to reversibly sample an ensemble of similarly stable native states. Such perspectives suggest that substrates, factors and environmental cues contribute to translation regulation by helping the dynamic system navigate through a highly complex and metastable energy landscape. Author Affiliation: (1) Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10021, USA (2) Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Mail Stop K710, T-10, Los Alamos, NM 87545, USA (3) Institut fur Medizinische Physik und Biophysik, Charite-Universitatsmedizin Berlin, Ziegelstrasse 5-9, 10117 Berlin, Germany

Published
2009

46. Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity

Author

Palmateer, Nicholas C., primary, Tretina, Kyle, additional, Orvis, Joshua, additional, Ifeonu, Olukemi O., additional, Crabtree, Jonathan, additional, Drabék, Elliott, additional, Pelle, Roger, additional, Awino, Elias, additional, Gotia, Hanzel T., additional, Munro, James B., additional, Tallon, Luke, additional, Morrison, W. Ivan, additional, Daubenberger, Claudia A., additional, Nene, Vish, additional, Knowles, Donald P., additional, Bishop, Richard P., additional, and Silva, Joana C., additional

Published
2020
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47. Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant

Author

Yurkovetskiy, Leonid, primary, Wang, Xue, additional, Pascal, Kristen E., additional, Tomkins-Tinch, Christopher, additional, Nyalile, Thomas P., additional, Wang, Yetao, additional, Baum, Alina, additional, Diehl, William E., additional, Dauphin, Ann, additional, Carbone, Claudia, additional, Veinotte, Kristen, additional, Egri, Shawn B., additional, Schaffner, Stephen F., additional, Lemieux, Jacob E., additional, Munro, James B., additional, Rafique, Ashique, additional, Barve, Abhi, additional, Sabeti, Pardis C., additional, Kyratsous, Christos A., additional, Dudkina, Natalya V., additional, Shen, Kuang, additional, and Luban, Jeremy, additional

Published
2020
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