Search Results - "Computational platforms and environments"

A universal language for finding mass spectrometry data patterns

Authors: Tito Damiani Alan K. Jarmusch Allegra T. Aron et al.

Source: Nature methods
Nature Methods, vol 22, iss 6

Subject Terms: Computer. Automation, Technology, Bioengineering, Biological Sciences, Medical and Health Sciences, Mass Spectrometry, Biological sciences, Networking and Information Technology R&D (NITRD), Computational platforms and environments, mass spectrometry data, Biowissenschaften, Biologie, Data Mining, Humans, Life Science, Metabolomics, Programming Languages, Software, Developmental Biology

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/40355727
https://hdl.handle.net/10067/2153130151162165141
https://research.wur.nl/en/publications/a-universal-language-for-finding-mass-spectrometry-data-patterns
https://doi.org/10.1038/s41592-025-02660-z
https://escholarship.org/uc/item/28x5h3tn
https://escholarship.org/content/qt28x5h3tn/qt28x5h3tn.pdf

The HADDOCK2.4 web server for integrative modeling of biomolecular complexes

Authors: Rodrigo V. Honorato Mikael E. Trellet Brian Jiménez-García et al.

Contributors: Rodrigo V. Honorato Mikael E. Trellet Brian Jiménez-García et al.

Source: Digital.CSIC. Repositorio Institucional del CSIC
Consejo Superior de Investigaciones Científicas (CSIC)

Subject Terms: Models, Molecular, 0301 basic medicine, Technology, Internet, 0303 health sciences, ddc:600, Macromolecular Substances, General Biochemistry,Genetics and Molecular Biology, Computational Biology, Review, Antigen-Antibody Complex, Nucleosomes, 03 medical and health sciences, Computational platforms and environments, Journal Article, Molecular modelling, Software

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/38886530
http://hdl.handle.net/10261/384439
https://research-portal.uu.nl/en/publications/14d1d7fc-35c7-41ca-a6d0-05b9925f9934
https://doi.org/10.1038/s41596-024-01011-0
https://dspace.library.uu.nl/handle/1874/457978

SpatialData: an open and universal data framework for spatial omics

Authors: Luca Marconato Giovanni Palla Kevin A. Yamauchi et al.

Source: Nat Methods
Nature Methods, 22 (1)
NATURE METHODS

Subject Terms: Computational platforms and environments, Data integration, Molecular imaging, Software, SINGLE-CELL, Medicine and Health Sciences, Biology and Life Sciences, Brief Communication, 3. Good health

File Description: application/application/pdf; application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/38509327
http://hdl.handle.net/20.500.11850/667300
https://biblio.ugent.be/publication/01HY3FM5241PC97AF2F5B5VZQC
http://doi.org/10.1038/s41592-024-02212-x
http://hdl.handle.net/1854/LU-01HY3FM5241PC97AF2F5B5VZQC
https://biblio.ugent.be/publication/01HY3FM5241PC97AF2F5B5VZQC/file/01JHNBCCCRM8BW79PQARKVV2YZ

A universal language for finding mass spectrometry data patterns

Authors: Damiani, Tito Jarmusch, Alan K. Aron, Allegra T. et al.

Subject Terms: Computational platforms and environments, Metabolomics, mass spectrometry data, ddc:570

File Description: 12 Seiten; application/pdf

Availability: https://refubium.fu-berlin.de/handle/fub188/48914
https://doi.org/10.17169/refubium-48637
https://doi.org/10.1038/s41592-025-02660-z

SpatialData: an open and universal data framework for spatial omics

Authors: Marconato, Luca Palla, Giovanni Yamauchi, Kevin A. et al.

Source: Nature Methods, 22 (1)

Subject Terms: Computational platforms and environments, Data integration, Molecular imaging, Software

File Description: application/application/pdf

Relation: info:eu-repo/semantics/altIdentifier/wos/001188190200002; http://hdl.handle.net/20.500.11850/667300

Availability: https://hdl.handle.net/20.500.11850/667300
https://doi.org/10.3929/ethz-b-000667300

Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures

Authors: Kwon, Seulki Safer, Jordan Nguyen, Duyen T. et al.

Contributors: Kwon, Seulki Safer, Jordan Nguyen, Duyen T. et al.

Source: Nature Methods (2024-09-18)

Subject Terms: Computational platforms and environments, Data integration, Databases, Proteome informatics, Life sciences, Genetics & genetic processes, Sciences du vivant, Génétique & processus génétiques

Relation: https://doi.org/10.1038/s41592-024-02409-0; urn:issn:1548-7091; urn:issn:1548-7105; https://orbilu.uni.lu/handle/10993/62062; info:hdl:10993/62062; https://orbilu.uni.lu/bitstream/10993/62062/1/Kwon2024.NatMethods.pdf

Availability: https://orbilu.uni.lu/handle/10993/62062
https://orbilu.uni.lu/bitstream/10993/62062/1/Kwon2024.NatMethods.pdf
https://doi.org/10.1038/s41592-024-02409-0

Overlay databank unlocks data-driven analyses of biomolecules for all

Authors: Kiirikki, Anne M. Antila, Hanne S. Bort, Lara S. et al.

Contributors: Kiirikki, Anne M. Antila, Hanne S. Bort, Lara S. et al.

Source: Nat Commun
Nature Communications, Vol 15, Iss 1, Pp 1-15 (2024)
Nature Communications
Research Square
Nature Communications 15(1), 1136 (2024). doi:10.1038/s41467-024-45189-z
Nature Communications 15, 1136 (2024). doi:10.1038/s41467-024-45189-z

Subject Terms: Simulations, 0301 basic medicine, databases, Science, tekoäly, Molecular Dynamics Simulation, biofysiikka, Article, Lipid-bilayers, Scattering, Diffusion, Machine Learning, Membrane Lipids, 03 medical and health sciences, Orgaaninen kemia, Artificial Intelligence, [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], tietokannat, biological physics, 11832 Microbiology and virology, Flip-flop, 0303 health sciences, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Organic Chemistry, Cell Membrane, [INFO.INFO-LG] Computer Science [cs]/Machine Learning [cs.LG], laskennallinen kemia, computational chemistry, Nmr, Dynamics, Phosphatidylcholine, computational platforms and environments, Chemical sciences, Nanoscience Center, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, membrane biophysics, Molecular-structures, Model

File Description: application/pdf; fulltext

Access URL: https://pubmed.ncbi.nlm.nih.gov/38326316
https://doaj.org/article/acfa193917a24cbab8ffde269f7d7c0d
http://urn.fi/URN:NBN:fi:jyu-202402191951
http://hdl.handle.net/10138/573375
http://hdl.handle.net/21.11116/0000-000E-7486-8
http://hdl.handle.net/21.11116/0000-000E-7488-6
https://juser.fz-juelich.de/record/1025607
https://publications.rwth-aachen.de/record/985118
https://hdl.handle.net/11250/3170794

Ontology for the Avida digital evolution platform

Authors: Ortega, Raúl Wulff, Enrique Fortuna, Miguel et al.

Contributors: Ortega, Raúl Wulff, Enrique Fortuna, Miguel et al.

Source: Sci Data
Digital.CSIC. Repositorio Institucional del CSIC
Consejo Superior de Investigaciones Científicas (CSIC)
Scientific Data, Vol 10, Iss 1, Pp 1-9 (2023)

Subject Terms: Plataformas y entornos computacionales, Computational platforms and environments, Science, Ontologies, Ontologías, Software, Article, Plateformes et environnements informatiques, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/37689762
https://api.elsevier.com/content/abstract/scopus_id/85170343636
http://hdl.handle.net/10261/340591
https://hal.science/hal-04211072v1
https://doi.org/10.1038/s41597-023-02514-3
https://doaj.org/article/bf2aebaa12a2416489f6fc6873eaff1c

HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search

Authors: Yi-Yuan Lee Mustafa Guler Desnor N. Chigumba et al.

Source: Nat Commun
Nature Communications, Vol 14, Iss 1, Pp 1-17 (2023)

Subject Terms: ddc:004, Biological Products, Natural products, Databases, Factual, Science, Article, Tandem Mass Spectrometry, Computational platforms and environments, Drug discovery and development, Peptides, Ribosomes, Protein Processing, Post-Translational

Access URL: https://pubmed.ncbi.nlm.nih.gov/37452020
https://doaj.org/article/d0cd311036a049e799043f3d3049ff80

System theory computing elements comparison: two modelling examples towards sustainability

Authors: Heiden, Bernhard Tonino-Heiden, Bianca Alieksieiev, Volodymyr

Subject Terms: Computer Modelling, Computational platforms and environments, Ecological Modelling, Models of Computation, Systems Analysis, Theory of Computation, 6: Technology::600: Technology

Relation: Studies in systems, decision and control; https://hdl.handle.net/11420/58614

Availability: https://hdl.handle.net/11420/58614

Prediction of protein subplastid localization and origin with PlastoGram

Authors: Sidorczuk, Katarzyna Gagat, Przemysław Kała, Jakub et al.

Source: Sci Rep
Dipòsit Digital de Documents de la UAB
Universitat Autònoma de Barcelona
Scientific Reports, Vol 13, Iss 1, Pp 1-10 (2023)
Sidorczuk, K, Gagat, P, Kała, J, Nielsen, H, Pietluch, F, Mackiewicz, P & Burdukiewicz, M 2023, ' Prediction of protein subplastid localization and origin with PlastoGram ', Scientific Reports, vol. 13, no. 1, 8365 . https://doi.org/10.1038/s41598-023-35296-0

Subject Terms: Science, Genome, Plastid, Membrane Proteins, Molecular Sequence Annotation, Thylakoids, Article, Computational biology and bioinformatics, Chloroplast Proteins, Computational platforms and environments, Machine learning, Medicine, Protein analysis, Plant sciences, Software

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/37225726
https://doaj.org/article/bc376456615248e8a5e7560ed4b81cad
https://www.nature.com/articles/s41598-023-35296-0
https://doi.org/10.1038/s41598-023-35296-0
https://orbit.dtu.dk/en/publications/963b7ff1-5cd7-4042-92f8-5a452ce2e980
https://ddd.uab.cat/record/286216

Critical Assessment of Protein Intrinsic Disorder Prediction

Authors: Necci, Marco Piovesan, Damiano Tosatto, Silvio et al.

Contributors: Necci, Marco Piovesan, Damiano Tosatto, Silvio et al.

Source: Nat Methods
CONICET Digital (CONICET)
Consejo Nacional de Investigaciones Científicas y Técnicas
Nature Methods

Subject Terms: 0301 basic medicine, Protein Folding, Biomedical and clinical sciences, disorder prediction, Protein Conformation, 631/45/612, analysis, [INFO] Computer Science [cs], 03 medical and health sciences, Computational platforms and environments, 631/114/2398, Machine learning, 631/114/2411, Amino Acid Sequence, Databases, Protein, 0303 health sciences, Intrinsically disordered proteins, Proteins, Computational Biology, disorder, 631/114/1305, 3. Good health, [SDV] Life Sciences [q-bio], Intrinsically Disordered Proteins, Biological sciences, CAID, Protein structure predictions, 631/114/794, Software, Analysis, Protein Binding

File Description: application/pdf; text/xml

Access URL: https://www.nature.com/articles/s41592-021-01117-3.pdf
https://pubmed.ncbi.nlm.nih.gov/33875885
https://www.biorxiv.org/content/10.1101/2020.08.11.245852v1
https://www.biorxiv.org/content/biorxiv/early/2020/08/12/2020.08.11.245852.full.pdf
https://vinar.vin.bg.ac.rs/handle/123456789/9698
https://www.nature.com/articles/s41592-021-01117-3.pdf
https://research-repository.griffith.edu.au/handle/10072/404324
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8105172
https://pubmed.ncbi.nlm.nih.gov/33875885/
https://www.nature.com/articles/s41592-021-01117-3
https://hal.sorbonne-universite.fr/hal-03329755v2
https://hal.sorbonne-universite.fr/hal-03329755v2/document
https://doi.org/10.1038/s41592-021-01117-3
http://hdl.handle.net/11336/143754
https://hdl.handle.net/11577/3390525
https://doi.org/10.1038/s41592-021-01117-3
https://vinar.vin.bg.ac.rs/handle/123456789/9698
https://vinar.vin.bg.ac.rs/bitstream/id/24849/s41592-021-01117-3.pdf
https://discovery-pp.ucl.ac.uk/id/eprint/10127936/

Butler enables rapid cloud-based analysis of thousands of human genomes

Authors: Sergei Yakneen Sebastian M. Waszak Brice Aminou et al.

Contributors: Sergei Yakneen Sebastian M. Waszak Brice Aminou et al.

Source: Nat Biotechnol
Dipòsit Digital de la UB
Universidad de Barcelona
Articles publicats en revistes (Bioquímica i Biomedicina Molecular)
Nature Biotechnology, 38, 3, pp. 288-29210.1038/s41587-019-0360-3.
Weischenfeldt, J, PCAWG Technical Working Group & PCAWG Consortium 2020, ' Butler enables rapid cloud-based analysis of thousands of human genomes ', Nature Biotechnology, vol. 38, no. 3, pp. 288-292 . https://doi.org/10.1038/s41587-019-0360-3
Nature Biotechnology, vol 38, iss 3

Subject Terms: 0301 basic medicine, Radboudumc 17: Women's cancers Laboratory Medicine, Radboudumc 17: Women's cancers Radiation Oncology, 0206 medical engineering, 02 engineering and technology, Genome informatics, Genoma humà, Brief Communication, Biologia computacional, Computational biology, 03 medical and health sciences, Ecology,Evolution & Ethology, Computational platforms and environments, Neoplasms, Genetics, Humans, Hardware and infrastructure, Cancer, Computational Biology/methods, Neoplasms/genetics, Humans [MeSH], Software [MeSH], Genome, Human, Cloud Computing, Software, Neoplasms/genetics [MeSH], Cloud Computing [MeSH], Genome, Human [MeSH], Computational Biology/methods [MeSH], Computational & Systems Biology, VARIANT DISCOVERY, ddc:610, Human Biology & Physiology, Genome, Science & Technology, Human genome, Human Genome, PCAWG Consortium, Computational Biology, Tumour Biology, 3. Good health, Data processing, Laboratory Medicine - Radboud University Medical Center, Biotechnology & Applied Microbiology, PCAWG Technical Working Group, Life Sciences & Biomedicine, Genetics & Genomics, Human

File Description: application/pdf; text/xml; application/zip

Access URL: https://europepmc.org/articles/pmc7062635?pdf=render
https://pubmed.ncbi.nlm.nih.gov/32024987
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https://hdl.handle.net/2445/172342
https://hdl.handle.net/https://repository.ubn.ru.nl/handle/2066/291223
https://www.nature.com/articles/s41587-019-0360-3
https://doi.org/10.1038/s41587-019-0360-3
https://escholarship.org/uc/item/2gg6377p
https://www.nature.com/articles/s41587-019-0360-3.pdf
https://www.mendeley.com/catalogue/227980c9-cf2c-3c1f-85d0-564a2809d6f1/
https://www.nature.com/articles/s41587-019-0360-3
https://www.research-collection.ethz.ch/handle/20.500.11850/400227
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https://curis.ku.dk/ws/files/256937017/s41587_019_0360_3.pdf
https://nbn-resolving.org/urn:nbn:de:bvb:384-opus4-923946
https://doi.org/10.1038/s41587-019-0360-3
https://opus.bibliothek.uni-augsburg.de/opus4/frontdoor/index/index/docId/92394
https://opus.bibliothek.uni-augsburg.de/opus4/files/92394/92394.pdf
https://www.nature.com/articles/s41587-019-0360-3#Sec13
https://escholarship.org/content/qt2gg6377p/qt2gg6377p.pdf
https://escholarship.org/uc/item/2gg6377p

SeqTU: A web server for identification of bacterial transcription units

Contributors: Xu, Ying [Jilin Univ., Jilin (China); Univ. of Georgia, Athens, GA (United States); BioEnergy Science Center, Washington, D.C. (United States)]

Source: Scientific Reports; 7

File Description: Medium: ED; Size: Article No. 43925

Access URL: http://www.osti.gov/scitech/servlets/purl/1355909

Deep learning-based image analysis identifies a DAT-negative subpopulation of dopaminergic neurons in the lateral Substantia nigra

Authors: Burkert, Nicole Roy, Shoumik Häusler, Max et al.

Subject Terms: Computational platforms and environments, Ion channels in the nervous system, Machine learning, Molecular neuroscience, Neurophysiology

File Description: application/pdf

Availability: https://doi.org/10.18725/OPARU-54054
http://nbn-resolving.de/urn:nbn:de:bsz:289-oparu-54130-9

InterCellar enables interactive analysis and exploration of cell−cell communication in single-cell transcriptomic data

Authors: Interlandi, M. (Marta) Kerl, K.T. (Kornelius) Dugas, M. (Martin) et al.

Contributors: Interlandi, M. (Marta) Kerl, K.T. (Kornelius) Dugas, M. (Martin) et al.

Subject Terms: Communication and replication, Computational platforms and environments, Software, ddc:610, info:eu-repo/classification/ddc/610, Medicine and health

File Description: application/pdf

Relation: info:eu-repo/semantics/reference/url/https://static-content.springer.com/esm/art%3A10.1038%2Fs42003-021-02986-2/MediaObjects/42003_2021_2986_MOESM1_ESM.pdf; info:eu-repo/semantics/reference/url/https://static-content.springer.com/esm/art%3A10.1038%2Fs42003-021-02986-2/MediaObjects/42003_2021_2986_MOESM2_ESM.pdf; info:eu-repo/semantics/reference/url/https://static-content.springer.com/esm/art%3A10.1038%2Fs42003-021-02986-2/MediaObjects/42003_2021_2986_MOESM3_ESM.pdf; info:eu-repo/semantics/reference/url/https://static-content.springer.com/esm/art%3A10.1038%2Fs42003-021-02986-2/MediaObjects/42003_2021_2986_MOESM4_ESM.xlsx; info:eu-repo/semantics/reference/url/https://static-content.springer.com/esm/art%3A10.1038%2Fs42003-021-02986-2/MediaObjects/42003_2021_2986_MOESM5_ESM.pdf

Availability: https://nbn-resolving.org/urn:nbn:de:hbz:6-39928574727
https://doi.org/10.17879/79928457652
https://miami.uni-muenster.de/Record/31e4e8a9-456b-43b4-a942-b9b4f3dc651a
https://repositorium.uni-muenster.de/transfer/miami/31e4e8a9-456b-43b4-a942-b9b4f3dc651a

HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search

Authors: Lee, Yi-Yuan Guler, Mustafa Chigumba, Desnor N. et al.

Subject Terms: ddc:004, Computational platforms and environments, Drug discovery and development, Natural products, Peptides

Relation: https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-023-39905-4/MediaObjects/41467_2023_39905_MOESM1_ESM.pdf; https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-023-39905-4/MediaObjects/41467_2023_39905_MOESM2_ESM.pdf; hdl:20.500.11880/36974

Availability: http://nbn-resolving.org/urn:nbn:de:bsz:291--ds-412231
https://doi.org/10.22028/D291-41223
https://doi.org/10.1038/s41467-023-39905-4

Mic: A Deep Learning Tool for Assigning Ions and Waters in Cryo-Em and Crystal Structures

Authors: Shub, Laura Liu, Wenjin Skiniotis, Georgios et al.

Source: Faculty and Staff Publications

Subject Terms: Deep Learning, Cryoelectron Microscopy, Water, Crystallography, X-Ray, Ions, Models, Molecular, Proteins, Protein structure predictions, Computational biophysics, Data processing, Computational platforms and environments, Medical Sciences, Medical Specialties, Medicine and Health Sciences

File Description: application/pdf

Relation: https://digitalcommons.library.tmc.edu/baylor_docs/3851; https://digitalcommons.library.tmc.edu/context/baylor_docs/article/4779/viewcontent/41467_2025_Article_61315_compressed.pdf

Availability: https://digitalcommons.library.tmc.edu/baylor_docs/3851
https://doi.org/10.1038/s41467-025-61315-x
https://digitalcommons.library.tmc.edu/context/baylor_docs/article/4779/viewcontent/41467_2025_Article_61315_compressed.pdf

A Visual-Omics Foundation Model To Bridge Histopathology With Spatial Transcriptomics

Authors: Chen, Weiqing Zhang, Pengzhi Tran, Tu N et al.

Source: Faculty, Staff and Student Publications

Subject Terms: Humans, Transcriptome, Computational Biology, Gene Expression Profiling, Genomics, Image Processing, Computer-Assisted, Artificial Intelligence, Single-Cell Analysis, Computational models, Software, Machine learning, Computational platforms and environments, Bioinformatics, Biomedical Informatics, Genetic Phenomena, Medical Genetics, Medical Sciences, Medical Specialties, Medicine and Health Sciences, Oncology

File Description: application/pdf

Relation: https://digitalcommons.library.tmc.edu/uthgsbs_docs/4199; https://digitalcommons.library.tmc.edu/context/uthgsbs_docs/article/5099/viewcontent/41592_2025_Article_2707_compressed.pdf

Availability: https://digitalcommons.library.tmc.edu/uthgsbs_docs/4199
https://doi.org/10.1038/s41592-025-02707-1
https://digitalcommons.library.tmc.edu/context/uthgsbs_docs/article/5099/viewcontent/41592_2025_Article_2707_compressed.pdf

OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies

Authors: Josh Moore Chris Allan Sébastien Besson et al.

Contributors: Josh Moore Chris Allan Sébastien Besson et al.

Source: Nat Methods

Subject Terms: 0301 basic medicine, Databases, Factual, 0206 medical engineering, Information Storage and Retrieval, 02 engineering and technology, Brief Communication, Data publication and archiving, name=Cell Biology, 03 medical and health sciences, Computational platforms and environments, Internet, Metadata, Microscopy, SARS-CoV-2, name=Biochemistry, Computational Biology, name=Biotechnology, name=Molecular Biology, Data Compression, Programming Languages, Software

File Description: application/pdf

Access URL: https://www.nature.com/articles/s41592-021-01326-w.pdf
https://pubmed.ncbi.nlm.nih.gov/34845388
https://resolver.sub.uni-goettingen.de/purl?gro-2/106405