Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
273
datasets available to search
ShareScore release 0.9.0
Dataset results
273 results for “Systems Biology”
Data from: Linking phenology to mating system: exploring the reproductive biology of the threatened palm species Butia eriospatha
Open the record for dataset details and reuse information.
List of papers reviewed to uncover trends in the use of model systems in infectious disease ecology & evolutionary biology
Open the record for dataset details and reuse information.
Data from: How biological attention mechanisms improve task performance in a large-scale visual system model
Open the record for dataset details and reuse information.
Supplementary material 1 from: Cunha MR, Génio L, Pradillon F, Clavel Henry M, Beaulieu S, Birch J, Campuzano FJ, Carretón M, De Leo F, Gula J, Laming S, Lindsay D, Matos FL, Metaxas A, Meyer-Kaiser K, Mills S, Queiroga H, Rodrigues CF, Sarrazin J, Watanabe H, Young R, Young CM (2020) Foresight Workshop on Advances in Ocean Biological Observations: a sustained system for deep-ocean meroplankton. Research Ideas and Outcomes 6: e54284. https://doi.org/10.3897/rio.6.e54284
Abstracts of keynote talks
Figure 2 from: Cunha MR, Génio L, Pradillon F, Clavel Henry M, Beaulieu S, Birch J, Campuzano FJ, Carretón M, De Leo F, Gula J, Laming S, Lindsay D, Matos FL, Metaxas A, Meyer-Kaiser K, Mills S, Queiroga H, Rodrigues CF, Sarrazin J, Watanabe H, Young R, Young CM (2020) Foresight Workshop on Advances in Ocean Biological Observations: a sustained system for deep-ocean meroplankton. Research Ideas and Outcomes 6: e54284. https://doi.org/10.3897/rio.6.e54284
Figure 2 Sustained meroplankton observations - a basin-scale approach. Low-cost samplers for deep-ocean observations (colonization modules coupled with larval traps) deployed at moorings or mounted on landers of the EMSO-ERIC distributed observatories and covering different water masses (Project LO3CATED; Génio, Cunha and Young). NACW: North Atlantic Central Water; AIW: Antarctic Intermediate Water; MOW: Mediterranean Outflow Water; NADW: North Atlantic Deep Water; MABW: Modified Antarctic Bottom Water.
Figure 1 from: Cunha MR, Génio L, Pradillon F, Clavel Henry M, Beaulieu S, Birch J, Campuzano FJ, Carretón M, De Leo F, Gula J, Laming S, Lindsay D, Matos FL, Metaxas A, Meyer-Kaiser K, Mills S, Queiroga H, Rodrigues CF, Sarrazin J, Watanabe H, Young R, Young CM (2020) Foresight Workshop on Advances in Ocean Biological Observations: a sustained system for deep-ocean meroplankton. Research Ideas and Outcomes 6: e54284. https://doi.org/10.3897/rio.6.e54284
Figure 1 Workshop participants "under the microscope" at the campus of Universidade de Aveiro: Back row, left to right: Fábio Matos, Jonathan Gula, Henrique Queiroga, Rob Young, Sven Laming, Kirstin Meyer-Kaiser, Jozée Sarrazin, Craig M. Young, Fabio De Leo. Front row, left to right: Jim Birch, Morane Clavel Henry, Marina R. Cunha, Clara Rodrigues, Florence Pradillon, Anna Metaxas.
Figure 1 from: Ferreira RL, Giribet G, Du Preez G, Ventouras O, Janion C, Silva MS (2020) The Wynberg Cave System, the most important site for cave fauna in South Africa at risk. Subterranean Biology 36: 73-81. https://doi.org/10.3897/subtbiol.36.60162
Figure 1 Wynberg Cave System and some troglomorphic taxa: APeripatopsis alba (Onycophora: Peripatopsidae) BSpelaeogriphus lepidops (Spelaeogriphacea: Spelaeogriphidae) CParamelita capensis (Amphipoda: Paramelitidae) DTrichoniscus tabulae (Isopoda: Trichoniscidae) EHarpethrix caeca (Diplopoda: Dalodesmidae) FHahnia sp. (Araneae: Hahniidae) GPurcellia argasiformis (Opiliones: Pettalidae) HSpeleomontia cavernicola (Opiliones: Triaenonychidae) IGymnobisium inukshuk (Pseudoscorpiones: Gymnobisiidae) JJapygidae sp.n (Diplura) KProrhynchus cf. brincki (Platyhelminthes: Prorhynchida). Photographs A, C–E, G, H, J from Rodrigo Ferreira; photographs B, I, K from Gonzalo Giribet; photograph F from Peter Swart.
Figure 2 from: Ferreira RL, Giribet G, Du Preez G, Ventouras O, Janion C, Silva MS (2020) The Wynberg Cave System, the most important site for cave fauna in South Africa at risk. Subterranean Biology 36: 73-81. https://doi.org/10.3897/subtbiol.36.60162
Figure 2 A External landscape surrounding the WCSB one of the entrances of the Wynberg cave C graffiti on the walls of Wynberg cave D Dead bat pending on the cave wall EPurcellia argasiformis with a parasitic mite attached to the first leg. Photographs A, B from Rodrigo Ferreira; photographs C, D from Oresti Ventouras; photograph E from Gonzalo Giribet.
Data from: Mutation rules and the evolution of sparseness and modularity in biological systems
Biological systems exhibit two structural features on many levels of organization: sparseness, in which only a small fraction of possible interactions between components actually occur; and modularity – the near decomposability of the system into modules with distinct functionality. Recent work suggests that modularity can evolve in a variety of circumstances, including goals that vary in time such that they share the same subgoals (modularly varying goals), or when connections are costly. Here, we studied the origin of modularity and sparseness focusing on the nature of the mutation process, rather than on connection cost or variations in the goal. We use simulations of evolution with different mutation rules. We found that commonly used sum-rule mutations, in which interactions are mutated by adding random numbers, do not lead to modularity or sparseness except for in special situations. In contrast, product-rule mutations in which interactions are mutated by multiplying by random numbers – a better model for the effects of biological mutations – led to sparseness naturally. When the goals of evolution are modular, in the sense that specific groups of inputs affect specific groups of outputs, product-rule mutations also lead to modular structure; sum-rule mutations do not. Product-rule mutations generate sparseness and modularity because they tend to reduce interactions, and to keep small interaction terms small.
Supplementary material 2 from: Schneider AS, Knüsel M, Altermatt F (2023) Assessment of occurrence, diversity, and biomass of macroinvertebrates in Swiss groundwater systems using citizen science data. Subterranean Biology 46: 147-164. https://doi.org/10.3897/subtbiol.46.112569
Detailed procedure for macroinvertebrate bio-area measurements
Supplementary material 3 from: Schneider AS, Knüsel M, Altermatt F (2023) Assessment of occurrence, diversity, and biomass of macroinvertebrates in Swiss groundwater systems using citizen science data. Subterranean Biology 46: 147-164. https://doi.org/10.3897/subtbiol.46.112569
Supplementary results
Supplementary material 1 from: Schneider AS, Knüsel M, Altermatt F (2023) Assessment of occurrence, diversity, and biomass of macroinvertebrates in Swiss groundwater systems using citizen science data. Subterranean Biology 46: 147-164. https://doi.org/10.3897/subtbiol.46.112569
Bio-area and biomass relationship
A systems biology approach to investigate glucocorticoid response in a cellular model of human bronchial epithelium - Supplementary material
<p>Electronic appendices of PhD thesis: "A systems biology approach to investigate glucocorticoid response in a cellular model of human bronchial epithelium".</p>
Figure 1 from: Sánchez-Fernández D, Rizzo V, Bourdeau C, Cieslak A, Comas J, Faille A, Fresneda J, Lleopart E, Millán A, Montes A, Pallares S, Ribera I (2018) The deep subterranean environment as a model system in ecological, biogeographical and evolutionary research. Subterranean Biology 25: 1-7. https://doi.org/10.3897/subtbiol.25.23530
Figure 1 Relationship between the temperature inside the cave and the surface (Mean Annual Temperature (°C) of each pixel (0.08° cells).
Figure 2 from: Benítez S, Illife TM, Quiroz-Martínez B, Alvarez F (2019) How is the anchialine fauna distributed within a cave? A study of the Ox Bel Ha System, Yucatan Peninsula, Mexico. Subterranean Biology 31: 15-28. https://doi.org/10.3897/subtbiol.31.34347
Figure 2 Ecological parameters of the anchialine fauna in the Ox Bel Ha anchialine cave system along a transect A mean ± one standard error of the abundance B mean ± one standard error of the species richness C Shannon's diversity index. The sites are: T, Tábano; O, Odyssey; M, Muknal; B, Bang.
Figure 1 from: Benítez S, Illife TM, Quiroz-Martínez B, Alvarez F (2019) How is the anchialine fauna distributed within a cave? A study of the Ox Bel Ha System, Yucatan Peninsula, Mexico. Subterranean Biology 31: 15-28. https://doi.org/10.3897/subtbiol.31.34347
Figure 1 Map of the Ox Bel Ha anchialine cave system near the town of Tulum. Quintana Roo, Mexico. The four cenotes used to access the cave were: Tábano, Odyssey, Muknal and Bang.
Figure 4 from: Benítez S, Illife TM, Quiroz-Martínez B, Alvarez F (2019) How is the anchialine fauna distributed within a cave? A study of the Ox Bel Ha System, Yucatan Peninsula, Mexico. Subterranean Biology 31: 15-28. https://doi.org/10.3897/subtbiol.31.34347
Figure 4 A Dendrogram and B non-metrical multidimensional scaling (nMDS) ordination plot, both resulting from the similarity matrix based on Jaccard's similarity index.
Figure 3 from: Benítez S, Illife TM, Quiroz-Martínez B, Alvarez F (2019) How is the anchialine fauna distributed within a cave? A study of the Ox Bel Ha System, Yucatan Peninsula, Mexico. Subterranean Biology 31: 15-28. https://doi.org/10.3897/subtbiol.31.34347
Figure 3 Distribution of organisms by species in relation to depth in the four cenotes studied in the Ox Bel Ha cave: A, cenote Tábano; B, cenote Odyssey; C, cenote Muknal; and D, cenote Bang. The red band depicts the halocline, its width represents the thickness of the interface.
Data from: Systems biology of tissue-specific response to Anaplasma phagocytophilum reveals differentiated apoptosis in the tick vector Ixodes scapularis
Anaplasma phagocytophilum is an emerging pathogen that causes human granulocytic anaplasmosis. Infection with this zoonotic pathogen affects cell function in both vertebrate host and the tick vector, Ixodes scapularis. Global tissue-specific response and apoptosis signaling pathways were characterized in I. scapularis nymphs and adult female midguts and salivary glands infected with A. phagocytophilum using a systems biology approach combining transcriptomics and proteomics. Apoptosis was selected for pathway-focused analysis due to its role in bacterial infection of tick cells. The results showed tissue-specific differences in tick response to infection and revealed differentiated regulation of apoptosis pathways. The impact of bacterial infection was more pronounced in tick nymphs and midguts than in salivary glands, probably reflecting bacterial developmental cycle. All apoptosis pathways described in other organisms were identified in I. scapularis, except for the absence of the Perforin ortholog. Functional characterization using RNA interference showed that Porin knockdown significantly increases tick colonization by A. phagocytophilum. Infection with A. phagocytophilum produced complex tissue-specific alterations in transcript and protein levels. In tick nymphs, the results suggested a possible effect of bacterial infection on the inhibition of tick immune response. In tick midguts, the results suggested that A. phagocytophilum infection inhibited cell apoptosis to facilitate and establish infection through up-regulation of the JAK/STAT pathway. Bacterial infection inhibited the intrinsic apoptosis pathway in tick salivary glands by down-regulating Porin expression that resulted in the inhibition of Cytochrome c release as the anti-apoptotic mechanism to facilitate bacterial infection. However, tick salivary glands may promote apoptosis to limit bacterial infection through induction of the extrinsic apoptosis pathway. These dynamic changes in response to A. phagocytophilum in I. scapularis tissue-specific transcriptome and proteome demonstrated the complexity of the tick response to infection and will contribute to characterize gene regulation in ticks.
Figure 2 from: Weigand A (2013) New Zospeum species (Gastropoda, Ellobioidea, Carychiidae) from 980 m depth in the Lukina Jama–Trojama cave system (Velebit Mts., Croatia). Subterranean Biology 11: 45-53. https://doi.org/10.3897/subtbiol.11.5966
Figure 2 - Holotype and paratypes of Zospeum tholussum. The holotype (former living specimen) is marked with a solid line; five paratype specimens (shells) are surrounded by dotted lines.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.