المؤلفون: Noelia Ferruz, Michael Heinzinger, Mehmet Akdel, Alexander Goncearenco, Luca Naef, Christian Dallago

المصدر: Computational and Structural Biotechnology Journal, Vol 21, Iss , Pp 238-250 (2023)

مصطلحات موضوعية: Protein design, Protein prediction, Drug discovery, Deep learning, Protein language models, Biotechnology, TP248.13-248.65

وصف الملف: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037022005086; https://doaj.org/toc/2001-0370

URL الوصول: https://doaj.org/article/551fa6fbd7244da18697eddc83db91c5

المؤلفون: Mehmet Akdel, Janani Durairaj, Dick de Ridder, Aalt D.J. van Dijk

المصدر: Computational and Structural Biotechnology Journal, Vol 18, Iss , Pp 981-992 (2020)

مصطلحات موضوعية: Structure alignment, Machine learning, Protein structure, Dynamic programming, Biotechnology, TP248.13-248.65

وصف الملف: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037019304477; https://doaj.org/toc/2001-0370

URL الوصول: https://doaj.org/article/9d5801ede6c74ba596617da056238853

المؤلفون: Mehmet Akdel, Henri van de Geest, Elio Schijlen, Irma M H van Rijswijck, Eddy J Smid, Gabino Sanchez-Perez, Dick de Ridder

المصدر: PLoS ONE, Vol 16, Iss 9, p e0253102 (2021)

مصطلحات موضوعية: Medicine, Science

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1932-6203

URL الوصول: https://doaj.org/article/e5b1890074b14452920ab733c5b1ad6f

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/journal_contribution/Estimated_time_required_to_compute_of_all-vs-all_OptiMap-naive_alignments_/16712114

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.s001

المؤلفون: Janani Durairaj, Andrew M. Waterhouse, Toomas Mets, Tetiana Brodiazhenko, Minhal Abdullah, Gabriel Studer, Mehmet Akdel, Antonina Andreeva, Alex Bateman, Tanel Tenson, Vasili Hauryliuk, Torsten Schwede, Joana Pereira

وصف الملف: application/pdf

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::786c91e64c9be50392c773c3fedf4cda
https://doi.org/10.1101/2023.03.14.532539

المؤلفون: Torsten Schwede, Joana Pereira, Mehmet Akdel, Janani Durairaj

وصف الملف: application/pdf

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::47b3f2be5d880f34e9b9bcc069b53de0
https://edoc.unibas.ch/90658/

المؤلفون: Mehmet Akdel, Dick de Ridder

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::7bb70a7ca1037f2ad8717202c4b99b99
https://doi.org/10.1101/2022.01.08.475501

المؤلفون: Irma M H van Rijswijck, Gabino F. Sanchez-Perez, Henri van de Geest, Eddy J. Smid, Mehmet Akdel, Dick de Ridder, Elio Schijlen

المصدر: PLoS ONE
PLoS ONE, Vol 16, Iss 9, p e0253102 (2021)
PLoS ONE 16 (2021) 9 September
PLoS ONE, 16(9 September)

مصطلحات موضوعية: Computer science, computer.software_genre, Levensmiddelenmicrobiologie, Database and Informatics Methods, Software, Cell Signaling, Optical Restriction Mapping, computer.programming_language, Multidisciplinary, Process (computing), Chromosome Mapping, High-Throughput Nucleotide Sequencing, Eukaryota, Software Engineering, Genomics, Medicine, Engineering and Technology, Data mining, Raw data, Sequence Analysis, Genomic Signal Processing, Research Article, Signal Transduction, Computer and Information Sciences, Bioinformatics, Science, Mycology, Research and Analysis Methods, Computer Software, BIOS Applied Bioinformatics, Optical mapping, Bioinformatica, Genetics, Life Science, Fungal Genetics, Molecular Biology Techniques, Molecular Biology, Fungal Genomics, VLAG, Assembly software, business.industry, SIGNAL (programming language), Gene Mapping, Organisms, Fungi, Biology and Life Sciences, Sequence Analysis, DNA, Cell Biology, Python (programming language), Yeast, Signal Processing, Food Microbiology, EPS, business, computer, Sequence Alignment

وصف الملف: application/pdf

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cec3fdace6bda5c5463e6e9589fa6e7a
https://pubmed.ncbi.nlm.nih.gov/34591846

المؤلفون: Janani Durairaj, Mehmet Akdel, Dick de Ridder, Aalt D. J. van Dijk

مصطلحات موضوعية: Structure (mathematical logic), Protein structure, Hierarchy (mathematics), Multiple structure alignment, Structural similarity, Computer science, business.industry, Structural alignment, Artificial intelligence, Machine learning, computer.software_genre, business, computer

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::bb100409ebfbe56cb260e2e6f036686c
https://doi.org/10.1101/2021.04.07.438777

المؤلفون: Pires Dev, Janet M. Thornton, Kundrotas P, Roman A. Laskowski, Jänes J, Tristan I. Croll, Rodrigues Chm, Mehmet Akdel, Sameer Velankar, Bryant P, Alistair Dunham, Durairaj J, Amelie Stein, Wensi Zhu, David F. Burke, Gabriele Pozzati, Norman E. Davey, Arthur O. Zalevsky, Alfonso Valencia, Porta Pardo E, Shenoy A, Liam Good, Sergey Ovchinnikov, Arne Elofsson, Kresten Lindorff-Larsen, Ruiz Serra, Pedro Beltrao, Bálint Mészáros, Adam Frost, David B. Ascher, Neera Borkakoti

المصدر: bioRxiv

مصطلحات موضوعية: Science research, Protein structure, Structural biology, Computer science, Protein Data Bank (RCSB PDB), Computational biology

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::20c1c69048708df07d4c63ccd4de3762

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/The_principle_of_BNG_optical_mapping_/16712117

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g001

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/OptiTools_workflow_/16712120

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g002

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/Frame_pairs_as_produced_by_the_BNG_platform_/16712123

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g003

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/Frame_stitching_/16712126

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g004

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/The_OptiMap_alignment_procedure_/16712129

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g005

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/Molecule_detection_yeast_by_OptiScan_and_BNG_/16712132

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g006

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/Comparison_of_3_different_contigs_assembled_by_the_BNG_assembler_using_molecules_extracted_by_OptiScan_and_by_BNG_software_/16712135

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g007

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/Distribution_of_alignment_overlap_lengths_for_pairs_aligned_only_by_either_of_the_tools_/16712141

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g009

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/Alignment_performance_for_yeast_A_and_eggplant_data_B_C_/16712138

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g008

المؤلفون: Mehmet Akdel (11507114), Henri van de Geest (3112641), Elio Schijlen (116974), Irma M. H. van Rijswijck (6110114), Eddy J. Smid (7525955), Gabino Sanchez-Perez (3500852), Dick de Ridder (17852)

مصطلحات موضوعية: Biochemistry, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, yield better assemblies, specific restriction sites, reference alignments using, range contiguity information, labeling approximately half, detect structural variation, assembly software accompanying, make full use, fluorescent dna backbone, bionano genomics software, laborious manual process, div >< p, bionano genomics platforms, unwound dna, higher use, tools lay, source methods, raw images, python implementations, publicly available, optimap results, optimap ), offer high, nl /<, measured signals

Relation: https://figshare.com/articles/figure/Visualization_of_overlapping_parts_of_molecule_pairs_aligned_by_A_OptiMap_and_B_RefAligner_/16712144

الاتاحة: https://doi.org/10.1371/journal.pone.0253102.g010