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    MathWorks Inc matlab the mathworks inc
    Matlab The Mathworks Inc, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 93/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/particle+swarm+optimization+algorithm+of+matlab+software/MATLAB+Grader/pmc09468110-96-75-77
    Average 93 stars, based on 11 article reviews
    matlab the mathworks inc - by Bioz Stars, 2026-09
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    Article Title: Microcontroller-Based Electronic Laboratory Measurement Device for Distance Education
    Article Snippet: Terauds, M.; Smolaninovs, V. The MATLAB Grader: Expanding Possibilities with Various Task Versions.

    Article Title: Semi-Automated Analysis of Dome-Shaped Macula in Preterm and Full-Term Infants Using Handheld Swept-Source Optical Coherence Tomography
    Article Snippet: A novel semi-automated program in MATLAB (MathWorks, Inc., Natick, MA, USA) measured the dome diameter by tangentially connecting the two points of the retinal pigment epithelium at the base of the dome, selected by the grader at the inflection point on each side (see ).

    Generated:

    Article Title: Phosphatidylserine exposure by developing astrocytes initiates microglia-mediated developmental cell death
    Article Snippet: .. OCTA images were processed and generated using custom MATLAB software, and cross-sectional B-scans were segmented automatically (using BabyDOCTRAP, Duke University, Durham, NC) followed by manual correction by experienced grader as previously reported ( ). ..

    Software:

    Article Title: Evaluating the reliability of a microperimetry-based method for assessing visual function in the junctional zone of geographic atrophy lesions
    Article Snippet: .. In brief, using custom MATLAB (MathWorks, Natick, Massachusetts) software, each grader (Grader 1 and Grader 2) registered baseline MP images (sensitivity maps superimposed on their respective scanning laser ophthalmoscopy (SLO) fundus images) to their corresponding baseline FAF images using fiducial markers manually positioned at corresponding bifurcations of the retinal vasculature. ..

    Article Title: Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network.
    Article Snippet: 3000656#sec020 (‘‘S2 Data’’) Ensembl Aken et al.91 https://www.ensembl.org/index.html GeneATLAS Canela-Xandri et al.54 http://geneatlas.roslin.ed.ac.uk gnomAD Genome Aggregation Database Karczewski et al.52 https://gnomad.broadinstitute.org GPCRdb Pandy-Szekeres et al.92 https://gpcrdb.org OMA Orthology Database Altenhoff et al.93 https://omabrowser.org/oma/home/ The Cancer Genome Atlas Cancer Genome Atlas Research94 https://portal.gdc.cancer.gov Experimental Models: Cell Lines Ready-to-Assay CCR3 Chemokine Receptor Frozen Cells Eurofins HTS008RTA Ready-to-Assay CCR10 Chemokine Receptor Frozen Cells Eurofins HTS014RTA HEK293T cells Abcam ab255449 De-identified human donor PBMCs Primary donor N/A Recombinant DNA CCR5 vectors (WT and mutants) This paper N/A CXCR4 vectors (WT and mutants) This paper N/A (Continued on next page) ll OPEN ACCESS Cell 188, 1–20.e1–e15, June 26, 2025 e3 Please cite this article in press as: Kleist et al., Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network, Cell (2025), https://doi.org/10.1016/j.cell.2025.03.046 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER ACKR1 vectors (WT and mutants) This paper N/A b-arrestin-1 vectors This paper Described in PMID: 35623707 pQE30-ACKR1 (1-60/C4A/C51A/C54A) Gutjahr et al.77 N/A pQE30-ACKR1 (1-60/C4A/G42D/C51A/C54A) This manuscript N/A pET28a-CCL28 Thomas et al.95 N/A pET28a-CCL28 (DS) This paper N/A pET28a-CCL28 (DSE) This paper N/A pET28a-CCL28 (DSEA) This paper N/A pET28a-CCL28 (DSEAI) This paper N/A pCL45.MND.P2A.ZsGreen This manuscript N/A GFP-FFLUC Hebbar et al.96 N/A Software and Algorithms Adobe Illustrator N/A https://www.adobe.com/products/illustrator.html ANNOVAR Wang et al.97 http://annovar.openbioinformatics.org/en/latest/ Bio3d Grant et al.98 http://thegrantlab.org/bio3d/ BD FACSDiva v 8.0 BD Biosciences N/A Clustal Omega Sievers et al.99 www.ebi.ac.uk/Tools/msa/clustalo/ Cytoscape version 3.7.1 Shannon et al.100 https://cytoscape.org FlowJo v10 BD Biosciences N/A GraphPad Prism GraphPad Software https://www.graphpad.com Incucyte 2022A Sartorius N/A Jalview Waterhouse et al.101 https://www.jalview.org/ KMAD algorithm Lange et al.102 https://www3.cmbi.umcn.nl/kmad/about/ MATLAB MathWorks https://www.mathworks.com/products/ matlab.html MstatX (trident scoring algorithm) Valdar103 https://github.com/gcollet/MstatX MUSCLE Edgar104 https://www.ebi.ac.uk/Tools/msa/muscle/ MUSTANG Konagurthu et al.105 http://lcb.infotech.monash.edu.au/mustang/ Protein Contact Atlas Kayikci et al.42 https://www.mrc-lmb.cam.ac.uk/pca/index.html PyMOL Schrödinger https://pymol.org/2/ R R Core Team https://cran.r-project.org R package ggseqlogo Wagih106 https://cran.r-project.org/web/packages/ ggseqlogo/index.html R package ggridges Wilke107 (https://wilkelab.org/ggridges/) Other Chemokine-GPCR web resource This paper https://andrewbkleist.github.io/chemokine_ gpcr_encoding/ AutoMACS Pro separator Miltenyi N/A FACS Canto II BD Biosciences N/A Incucyte Sartorius N/A CD4+ Microbeads Miltenyi 120000440 CD8+ Microbeads Miltenyi 130045201 AutoMACS Pro columns Miltenyi 130021101 Recovery Cell culture media Gibco 12648-010 RPMI1640 Cytiva SH30096.01 10% FBS GE Healthcare N/A 1% GlutaMAX Gibco 35050-061 Protamine sulfate N/A (Continued on next page) ll OPEN ACCESS e4 Cell 188, 1–20.e1–e15, June 26, 2025 Please cite this article in press as: Kleist et al., Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network, Cell (2025), https://doi.org/10.1016/j.cell.2025.03.046 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER PBS Corning 21-031-CV Reduced-growth factor Matrigel Corning CB-40230 MACS BSA Stock solution Miltenyi 130-091-376 E3X Repeater Pipette Eppendorf 4987000118 Combitip 0.1 ml pipette tip Eppendorf 30089510 Tissue culture flasks, T175 Corning 353112 Tissue culture flasks, T75 TRP 90076 6 well cell culture dish Falcon 353046 12 well cell culture dish Corning 3513 24 well cell culture dish TRP 92024 24 well non-tissue culture treated cell culture dish MidSci 667524 96 well cell culture dish Corning 3599 ll OPEN ACCESS Please cite this article in press as: Kleist et al., Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network, Cell (2025), https://doi.org/10.1016/j.cell.2025.03.046

    FACS:

    Article Title: Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network.
    Article Snippet: 3000656#sec020 (‘‘S2 Data’’) Ensembl Aken et al.91 https://www.ensembl.org/index.html GeneATLAS Canela-Xandri et al.54 http://geneatlas.roslin.ed.ac.uk gnomAD Genome Aggregation Database Karczewski et al.52 https://gnomad.broadinstitute.org GPCRdb Pandy-Szekeres et al.92 https://gpcrdb.org OMA Orthology Database Altenhoff et al.93 https://omabrowser.org/oma/home/ The Cancer Genome Atlas Cancer Genome Atlas Research94 https://portal.gdc.cancer.gov Experimental Models: Cell Lines Ready-to-Assay CCR3 Chemokine Receptor Frozen Cells Eurofins HTS008RTA Ready-to-Assay CCR10 Chemokine Receptor Frozen Cells Eurofins HTS014RTA HEK293T cells Abcam ab255449 De-identified human donor PBMCs Primary donor N/A Recombinant DNA CCR5 vectors (WT and mutants) This paper N/A CXCR4 vectors (WT and mutants) This paper N/A (Continued on next page) ll OPEN ACCESS Cell 188, 1–20.e1–e15, June 26, 2025 e3 Please cite this article in press as: Kleist et al., Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network, Cell (2025), https://doi.org/10.1016/j.cell.2025.03.046 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER ACKR1 vectors (WT and mutants) This paper N/A b-arrestin-1 vectors This paper Described in PMID: 35623707 pQE30-ACKR1 (1-60/C4A/C51A/C54A) Gutjahr et al.77 N/A pQE30-ACKR1 (1-60/C4A/G42D/C51A/C54A) This manuscript N/A pET28a-CCL28 Thomas et al.95 N/A pET28a-CCL28 (DS) This paper N/A pET28a-CCL28 (DSE) This paper N/A pET28a-CCL28 (DSEA) This paper N/A pET28a-CCL28 (DSEAI) This paper N/A pCL45.MND.P2A.ZsGreen This manuscript N/A GFP-FFLUC Hebbar et al.96 N/A Software and Algorithms Adobe Illustrator N/A https://www.adobe.com/products/illustrator.html ANNOVAR Wang et al.97 http://annovar.openbioinformatics.org/en/latest/ Bio3d Grant et al.98 http://thegrantlab.org/bio3d/ BD FACSDiva v 8.0 BD Biosciences N/A Clustal Omega Sievers et al.99 www.ebi.ac.uk/Tools/msa/clustalo/ Cytoscape version 3.7.1 Shannon et al.100 https://cytoscape.org FlowJo v10 BD Biosciences N/A GraphPad Prism GraphPad Software https://www.graphpad.com Incucyte 2022A Sartorius N/A Jalview Waterhouse et al.101 https://www.jalview.org/ KMAD algorithm Lange et al.102 https://www3.cmbi.umcn.nl/kmad/about/ MATLAB MathWorks https://www.mathworks.com/products/ matlab.html MstatX (trident scoring algorithm) Valdar103 https://github.com/gcollet/MstatX MUSCLE Edgar104 https://www.ebi.ac.uk/Tools/msa/muscle/ MUSTANG Konagurthu et al.105 http://lcb.infotech.monash.edu.au/mustang/ Protein Contact Atlas Kayikci et al.42 https://www.mrc-lmb.cam.ac.uk/pca/index.html PyMOL Schrödinger https://pymol.org/2/ R R Core Team https://cran.r-project.org R package ggseqlogo Wagih106 https://cran.r-project.org/web/packages/ ggseqlogo/index.html R package ggridges Wilke107 (https://wilkelab.org/ggridges/) Other Chemokine-GPCR web resource This paper https://andrewbkleist.github.io/chemokine_ gpcr_encoding/ AutoMACS Pro separator Miltenyi N/A FACS Canto II BD Biosciences N/A Incucyte Sartorius N/A CD4+ Microbeads Miltenyi 120000440 CD8+ Microbeads Miltenyi 130045201 AutoMACS Pro columns Miltenyi 130021101 Recovery Cell culture media Gibco 12648-010 RPMI1640 Cytiva SH30096.01 10% FBS GE Healthcare N/A 1% GlutaMAX Gibco 35050-061 Protamine sulfate N/A (Continued on next page) ll OPEN ACCESS e4 Cell 188, 1–20.e1–e15, June 26, 2025 Please cite this article in press as: Kleist et al., Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network, Cell (2025), https://doi.org/10.1016/j.cell.2025.03.046 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER PBS Corning 21-031-CV Reduced-growth factor Matrigel Corning CB-40230 MACS BSA Stock solution Miltenyi 130-091-376 E3X Repeater Pipette Eppendorf 4987000118 Combitip 0.1 ml pipette tip Eppendorf 30089510 Tissue culture flasks, T175 Corning 353112 Tissue culture flasks, T75 TRP 90076 6 well cell culture dish Falcon 353046 12 well cell culture dish Corning 3513 24 well cell culture dish TRP 92024 24 well non-tissue culture treated cell culture dish MidSci 667524 96 well cell culture dish Corning 3599 ll OPEN ACCESS Please cite this article in press as: Kleist et al., Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network, Cell (2025), https://doi.org/10.1016/j.cell.2025.03.046

    Cell Culture:

    Article Title: Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network.
    Article Snippet: 3000656#sec020 (‘‘S2 Data’’) Ensembl Aken et al.91 https://www.ensembl.org/index.html GeneATLAS Canela-Xandri et al.54 http://geneatlas.roslin.ed.ac.uk gnomAD Genome Aggregation Database Karczewski et al.52 https://gnomad.broadinstitute.org GPCRdb Pandy-Szekeres et al.92 https://gpcrdb.org OMA Orthology Database Altenhoff et al.93 https://omabrowser.org/oma/home/ The Cancer Genome Atlas Cancer Genome Atlas Research94 https://portal.gdc.cancer.gov Experimental Models: Cell Lines Ready-to-Assay CCR3 Chemokine Receptor Frozen Cells Eurofins HTS008RTA Ready-to-Assay CCR10 Chemokine Receptor Frozen Cells Eurofins HTS014RTA HEK293T cells Abcam ab255449 De-identified human donor PBMCs Primary donor N/A Recombinant DNA CCR5 vectors (WT and mutants) This paper N/A CXCR4 vectors (WT and mutants) This paper N/A (Continued on next page) ll OPEN ACCESS Cell 188, 1–20.e1–e15, June 26, 2025 e3 Please cite this article in press as: Kleist et al., Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network, Cell (2025), https://doi.org/10.1016/j.cell.2025.03.046 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER ACKR1 vectors (WT and mutants) This paper N/A b-arrestin-1 vectors This paper Described in PMID: 35623707 pQE30-ACKR1 (1-60/C4A/C51A/C54A) Gutjahr et al.77 N/A pQE30-ACKR1 (1-60/C4A/G42D/C51A/C54A) This manuscript N/A pET28a-CCL28 Thomas et al.95 N/A pET28a-CCL28 (DS) This paper N/A pET28a-CCL28 (DSE) This paper N/A pET28a-CCL28 (DSEA) This paper N/A pET28a-CCL28 (DSEAI) This paper N/A pCL45.MND.P2A.ZsGreen This manuscript N/A GFP-FFLUC Hebbar et al.96 N/A Software and Algorithms Adobe Illustrator N/A https://www.adobe.com/products/illustrator.html ANNOVAR Wang et al.97 http://annovar.openbioinformatics.org/en/latest/ Bio3d Grant et al.98 http://thegrantlab.org/bio3d/ BD FACSDiva v 8.0 BD Biosciences N/A Clustal Omega Sievers et al.99 www.ebi.ac.uk/Tools/msa/clustalo/ Cytoscape version 3.7.1 Shannon et al.100 https://cytoscape.org FlowJo v10 BD Biosciences N/A GraphPad Prism GraphPad Software https://www.graphpad.com Incucyte 2022A Sartorius N/A Jalview Waterhouse et al.101 https://www.jalview.org/ KMAD algorithm Lange et al.102 https://www3.cmbi.umcn.nl/kmad/about/ MATLAB MathWorks https://www.mathworks.com/products/ matlab.html MstatX (trident scoring algorithm) Valdar103 https://github.com/gcollet/MstatX MUSCLE Edgar104 https://www.ebi.ac.uk/Tools/msa/muscle/ MUSTANG Konagurthu et al.105 http://lcb.infotech.monash.edu.au/mustang/ Protein Contact Atlas Kayikci et al.42 https://www.mrc-lmb.cam.ac.uk/pca/index.html PyMOL Schrödinger https://pymol.org/2/ R R Core Team https://cran.r-project.org R package ggseqlogo Wagih106 https://cran.r-project.org/web/packages/ ggseqlogo/index.html R package ggridges Wilke107 (https://wilkelab.org/ggridges/) Other Chemokine-GPCR web resource This paper https://andrewbkleist.github.io/chemokine_ gpcr_encoding/ AutoMACS Pro separator Miltenyi N/A FACS Canto II BD Biosciences N/A Incucyte Sartorius N/A CD4+ Microbeads Miltenyi 120000440 CD8+ Microbeads Miltenyi 130045201 AutoMACS Pro columns Miltenyi 130021101 Recovery Cell culture media Gibco 12648-010 RPMI1640 Cytiva SH30096.01 10% FBS GE Healthcare N/A 1% GlutaMAX Gibco 35050-061 Protamine sulfate N/A (Continued on next page) ll OPEN ACCESS e4 Cell 188, 1–20.e1–e15, June 26, 2025 Please cite this article in press as: Kleist et al., Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network, Cell (2025), https://doi.org/10.1016/j.cell.2025.03.046 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER PBS Corning 21-031-CV Reduced-growth factor Matrigel Corning CB-40230 MACS BSA Stock solution Miltenyi 130-091-376 E3X Repeater Pipette Eppendorf 4987000118 Combitip 0.1 ml pipette tip Eppendorf 30089510 Tissue culture flasks, T175 Corning 353112 Tissue culture flasks, T75 TRP 90076 6 well cell culture dish Falcon 353046 12 well cell culture dish Corning 3513 24 well cell culture dish TRP 92024 24 well non-tissue culture treated cell culture dish MidSci 667524 96 well cell culture dish Corning 3599 ll OPEN ACCESS Please cite this article in press as: Kleist et al., Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network, Cell (2025), https://doi.org/10.1016/j.cell.2025.03.046



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